diff --git a/build.xml b/build.xml
index 834aef3cd..49efd616d 100644
--- a/build.xml
+++ b/build.xml
@@ -644,12 +644,8 @@
 
     <target name="sting-utils.jar" depends="gatk.compile, init.jar, R.public.tar, R.script.stage">
         <jar jarfile="${dist.dir}/StingUtils.jar">
-            <fileset dir="${java.classes}">
-              <include name="**/utils/**/*.class"/>
-              <exclude name="**/utils/codecs/vcf/**/*.class"/>
-              <exclude name="**/utils/variantcontext/**/*.class"/>
-            </fileset>
-            <fileset dir="${java.classes}" includes="**/commandline/**/*.class"/>
+            <fileset dir="${java.classes}" includes="**/sting/utils/**/*.class"/>
+            <fileset dir="${java.classes}" includes="**/sting/commandline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/pipeline/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/tools/**/*.class"/>
             <fileset dir="${java.classes}" includes="**/sting/jna/**/*.class"/>
@@ -659,7 +655,7 @@
                 <include name="**/${R.package.path}/**/*.tar.gz"/>
             </fileset>
             <fileset dir="${R.script.staging.dir}">
-                <include name="**/utils/**/*.R"/>
+                <include name="**/sting/utils/**/*.R"/>
             </fileset>
             <manifest>
                 <attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
@@ -667,14 +663,10 @@
         </jar>
     </target>
 
-    <target name="vcf.jar" depends="gatk.compile,init.jar">
-        <jar jarfile="${dist.dir}/vcf.jar">
+    <target name="variant.jar" depends="gatk.compile,init.jar">
+        <jar jarfile="${dist.dir}/variant.jar">
             <fileset dir="${java.classes}">
-              <include name="org/broadinstitute/sting/utils/codecs/vcf/**/*.class"/>
-              <include name="org/broadinstitute/sting/utils/codecs/bcf2/**/*.class"/>
-              <include name="org/broadinstitute/sting/utils/variantcontext/**/*.class"/>
-              <include name="org/broadinstitute/sting/utils/exceptions/**"/>
-	          <include name="org/broadinstitute/sting/utils/help/DocumentedGATKFeature.class"/>
+              <include name="org/broadinstitute/variant/**/*.class"/>
             </fileset>
         </jar>
     </target>
@@ -685,7 +677,7 @@
               <include name="org/broadinstitute/sting/utils/GenomeLocParser*.class"/>
               <include name="org/broadinstitute/sting/utils/GenomeLoc.class"/>
               <include name="org/broadinstitute/sting/utils/HasGenomeLocation.class"/>
-              <include name="org/broadinstitute/sting/utils/BaseUtils.class"/>
+              <include name="org/broadinstitute/variant/utils/BaseUtils.class"/>
               <include name="org/broadinstitute/sting/utils/Utils.class"/>
               <include name="org/broadinstitute/sting/utils/exceptions/**/*.class"/>
               <include name="org/broadinstitute/sting/gatk/walkers/na12878kb/core/**/*.class"/>
@@ -703,12 +695,12 @@
             <fileset dir="${java.contracts.dir}" />
             <fileset dir="${java.classes}">
 	          <include name="${resource.file}" />
-              <include name="**/gatk/**/*.class" />
-              <include name="**/alignment/**/*.class"/>
+              <include name="**/sting/gatk/**/*.class" />
+              <include name="**/sting/alignment/**/*.class"/>
             </fileset>
             <fileset dir="${R.script.staging.dir}">
-                <include name="**/gatk/**/*.R"/>
-                <include name="**/alignment/**/*.R"/>
+                <include name="**/sting/gatk/**/*.R"/>
+                <include name="**/sting/alignment/**/*.R"/>
             </fileset>
             <fileset dir="${key.dir}">
                 <include name="**/*.key"/>
@@ -719,7 +711,7 @@
         </jar>
 
         <jar jarfile="${dist.dir}/Aligner.jar">
-            <fileset dir="${java.classes}" includes="**/alignment/**/*.class" />
+            <fileset dir="${java.classes}" includes="**/sting/alignment/**/*.class" />
         </jar>
 
         <subant target="dist" genericantfile="build.xml">
@@ -755,7 +747,7 @@
         </jar>
     </target>
 
-    <target name="sting.jar" depends="sting-utils.jar, vcf.jar, gatk.jar, queue.jar" />
+    <target name="sting.jar" depends="sting-utils.jar, variant.jar, gatk.jar, queue.jar" />
 
     <target name="init.manifests" depends="sting.jar">
         <pathconvert property="jar.classpath" pathsep=" ">
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
index 94f6ff649..53f206bfe 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/downsampling/AlleleBiasedDownsamplingUtils.java
@@ -30,7 +30,8 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
index fc6d23382..30650e9c0 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ErrorModel.java
@@ -8,8 +8,8 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
index 303ab94d6..502853868 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoods.java
@@ -29,13 +29,13 @@ import net.sf.samtools.SAMUtils;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACcounts;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
 
 import java.util.*;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
index f6ad445c7..ce66ce8d0 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsCalculationModel.java
@@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
index 4bcaa5ff9..3b12fe475 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoods.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
index eb4cf1839..76a934091 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyIndelGenotypeLikelihoodsCalculationModel.java
@@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
index 0f0f85441..461329ad0 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoods.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMUtils;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.ExactACset;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
@@ -11,7 +11,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
index 9f2fdc096..3250de2b2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidySNPGenotypeLikelihoodsCalculationModel.java
@@ -31,7 +31,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
index 0a3512aa6..d6b3eb768 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceTest.java
@@ -10,10 +10,10 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SimpleTimer;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 
 import java.io.*;
 import java.util.*;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
index 6f3740ab3..f4f17f1e0 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcTestBuilder.java
@@ -4,7 +4,7 @@ import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
index b248c8759..5f5d80fde 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
@@ -27,9 +27,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 
 import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
@@ -532,7 +533,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
             }
 
             // if there is no mass on the (new) likelihoods, then just no-call the sample
-            if ( MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL ) {
+            if ( MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL ) {
                 newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
             }
             else {
@@ -544,7 +545,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
                     gb.PL(newLikelihoods);
 
                 // if we weren't asked to assign a genotype, then just no-call the sample
-                if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > VariantContextUtils.SUM_GL_THRESH_NOCALL )
+                if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > GATKVariantContextUtils.SUM_GL_THRESH_NOCALL )
                     gb.alleles(NO_CALL_ALLELES);
                 else
                     assignGenotype(gb, newLikelihoods, allelesToUse, ploidy);
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
index a786a860c..3b90370bc 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngine.java
@@ -36,7 +36,9 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -158,7 +160,7 @@ public class GenotypingEngine {
                 }
 
                 // Merge the event to find a common reference representation
-                final VariantContext mergedVC = VariantContextUtils.simpleMerge(genomeLocParser, eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
+                final VariantContext mergedVC = VariantContextUtils.simpleMerge(eventsAtThisLoc, priorityList, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, null, false, false);
                 if( mergedVC == null ) { continue; }
 
                 // let's update the Allele keys in the mapper because they can change after merging when there are complex events
@@ -200,7 +202,7 @@ public class GenotypingEngine {
                     VariantContext annotatedCall = annotationEngine.annotateContext(stratifiedReadMap, call);
 
                     if( annotatedCall.getAlleles().size() != mergedVC.getAlleles().size() ) { // some alleles were removed so reverseTrimming might be necessary!
-                        annotatedCall = VariantContextUtils.reverseTrimAlleles(annotatedCall);
+                        annotatedCall = GATKVariantContextUtils.reverseTrimAlleles(annotatedCall);
                     }
 
                     returnCalls.add( annotatedCall );
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
index 9744c3dd8..2f733a01a 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
@@ -48,8 +48,8 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.activeregion.ActiveRegionReadState;
 import org.broadinstitute.sting.utils.activeregion.ActivityProfileResult;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
@@ -61,8 +61,8 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.FileNotFoundException;
 import java.io.PrintStream;
@@ -238,7 +238,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         samplesList.addAll( samples );
         // initialize the UnifiedGenotyper Engine which is used to call into the exact model
         final UnifiedArgumentCollection UAC = new UnifiedArgumentCollection( SCAC ); // this adapter is used so that the full set of unused UG arguments aren't exposed to the HC user
-        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
+        UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
 
         // create a UAC but with the exactCallsLog = null, so we only output the log for the HC caller itself, if requested
         UnifiedArgumentCollection simpleUAC = new UnifiedArgumentCollection(UAC);
@@ -248,7 +248,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<Integer, Integer> implem
         simpleUAC.STANDARD_CONFIDENCE_FOR_EMITTING = Math.min( 4.0, UAC.STANDARD_CONFIDENCE_FOR_EMITTING ); // low values used for isActive determination only, default/user-specified values used for actual calling
         simpleUAC.CONTAMINATION_FRACTION = 0.0;
         simpleUAC.exactCallsLog = null;
-        UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
+        UG_engine_simple_genotyper = new UnifiedGenotyperEngine(getToolkit(), simpleUAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
 
         // initialize the output VCF header
         final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
index 8a401439b..0e4673497 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeResolver.java
@@ -39,18 +39,18 @@ import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.SWPairwiseAlignment;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.util.*;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
index 018102893..59f241cdb 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java
@@ -29,16 +29,13 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pairhmm.*;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
 
-import java.io.PrintStream;
 import java.util.*;
 
 public class LikelihoodCalculationEngine {
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
index bf6c82d82..6d5d268a6 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LocalAssemblyEngine.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.haplotypecaller;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.activeregion.ActiveRegion;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
index 3c5a1f79c..b0be5e757 100755
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssembler.java
@@ -11,8 +11,8 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.jgrapht.graph.DefaultDirectedGraph;
 
 import java.io.PrintStream;
diff --git a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
index 77a7c3bd9..4a13fb615 100644
--- a/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
+++ b/protected/java/src/org/broadinstitute/sting/utils/genotyper/AdvancedPerReadAlleleLikelihoodMap.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.downsampling.AlleleBiasedDownsamplingUtils;
 import org.broadinstitute.sting.utils.classloader.ProtectedPackageSource;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
index f95ba66b2..4d4dbbdb5 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/GeneralPloidyGenotypeLikelihoodsUnitTest.java
@@ -28,11 +28,11 @@ import net.sf.samtools.SAMUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
index 556b7451f..1b0ffbd26 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcPerformanceUnitTest.java
@@ -4,8 +4,8 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
index ee5436264..4753ad07a 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResultUnitTest.java
@@ -4,7 +4,7 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
index 7ee909fe0..6b53d6188 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcUnitTest.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
index 3df2f7883..0f2dc84dc 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/GeneralPloidyAFCalculationModelUnitTest.java
@@ -2,10 +2,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GeneralPloidyGenotypeLikelihoods;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
index 663471106..1293c274b 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalcUnitTest.java
@@ -3,10 +3,10 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
index 07e7b0d92..f44624a10 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/GenotypingEngineUnitTest.java
@@ -10,9 +10,9 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java
index 5652b118d..071c21f9e 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/haplotypecaller/SimpleDeBruijnAssemblerUnitTest.java
@@ -10,16 +10,11 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.genotyper.ArtificialReadPileupTestProvider;
 import org.broadinstitute.sting.utils.Haplotype;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
 import org.jgrapht.graph.DefaultDirectedGraph;
 import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.io.PrintStream;
 import java.util.*;
 
diff --git a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
index 6281054b1..4684d6d8a 100644
--- a/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
+++ b/protected/java/test/org/broadinstitute/sting/utils/pairhmm/PairHMMUnitTest.java
@@ -29,7 +29,7 @@ package org.broadinstitute.sting.utils.pairhmm;
 // the imports for unit testing.
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.testng.Assert;
 import org.testng.annotations.DataProvider;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java
index c63f5615f..db21411b3 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/Alignment.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/Alignment.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
index b903b9f7d..ef50cf088 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/AlignmentValidation.java
@@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
index 2d568a96a..67305ce78 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
@@ -4,7 +4,7 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.*;
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
diff --git a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
index fbeac9192..f29e639d6 100644
--- a/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
+++ b/public/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAJavaAligner.java
@@ -6,7 +6,7 @@ import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.reference.bwt.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 
 import java.io.File;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
index e0c2ce72a..5a1c2a1b4 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/DbsnpArgumentCollection.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.arguments;
 
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * @author ebanks
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
index 547f375bb..f8f1831f6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardCallerArgumentCollection.java
@@ -4,7 +4,7 @@ import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
index 4c0257e6a..72b01df01 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/arguments/StandardVariantContextInputArgumentCollection.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
 
 import org.broadinstitute.sting.commandline.Input;
 import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * @author ebanks
diff --git a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 34627b973..88f4166ef 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.contexts;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
index 8e4633869..2a7c5c7b2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/storage/VariantContextWriterStorage.java
@@ -30,14 +30,14 @@ import org.broad.tribble.AbstractFeatureReader;
 import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub;
 import org.broadinstitute.sting.gatk.refdata.tracks.FeatureManager;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.writer.Options;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.Options;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.*;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
index f521c959d..8a989b040 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VCFWriterArgumentTypeDescriptor.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.io.stubs;
 
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
index f92d78bb5..c512ba835 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/io/stubs/VariantContextWriterStub.java
@@ -29,13 +29,13 @@ import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.writer.Options;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.Options;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.File;
 import java.io.OutputStream;
@@ -232,7 +232,7 @@ public class VariantContextWriterStub implements Stub<VariantContextWriter>, Var
             }
 
             if ( UPDATE_CONTIG_HEADERS )
-                vcfHeader = VCFUtils.withUpdatedContigs(vcfHeader, engine);
+                vcfHeader = GATKVCFUtils.withUpdatedContigs(vcfHeader, engine);
         }
 
         outputTracker.getStorage(this).writeHeader(vcfHeader);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 5c7da82d0..8713e9797 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
index a2fe94641..0e0e8017d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManager.java
@@ -33,9 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.ReferenceDependentFeatureCodec;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.vcf.AbstractVCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.AbstractVCFCodec;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.GATKDocUtils;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
index 81fe73075..2bb6cbeee 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilder.java
@@ -39,7 +39,6 @@ import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet;
 import org.broadinstitute.sting.gatk.refdata.utils.RMDTriplet.RMDStorageType;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
index 3de85028f..91439b65f 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/samples/SampleDB.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.samples;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.Genotype;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
index e63dbcabd..93eaee209 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/ClipReads.java
@@ -37,7 +37,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.clipping.ClippingOp;
 import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
index 18bdb02ed..943a1147a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
@@ -32,12 +32,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
index 4d79c4112..4bda9a6d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalanceBySample.java
@@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.Collection;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
index aef3e49cf..e19e82597 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseCounts.java
@@ -37,10 +37,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
index e59fc827d..d234f3471 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/BaseQualityRankSumTest.java
@@ -2,11 +2,11 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
index 0c78c0204..5b1a1e236 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ChromosomeCounts.java
@@ -35,12 +35,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
index 1dff4d1a3..24da5e893 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ClippingRankSumTest.java
@@ -1,12 +1,12 @@
 package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
index c9481f244..97c61f056 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthOfCoverage.java
@@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
index 89a239e54..05c36eda6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/DepthPerAlleleBySample.java
@@ -7,17 +7,17 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
index 52072d10c..f0d46cf35 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/FisherStrand.java
@@ -34,13 +34,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
index 07391c78c..5994c1ab7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/GCContent.java
@@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index ca7180510..5ca3c9885 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -33,20 +33,20 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.Serializable;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
index 0340f457c..6a879db12 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
@@ -9,11 +9,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.WorkInProgressAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
index 037b357ae..ebeb10f43 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HomopolymerRun.java
@@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
index dd058b469..826b45fa0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/InbreedingCoeff.java
@@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
index c9a4d0ee6..cc42a7b35 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/LowMQ.java
@@ -6,10 +6,10 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
index c9d5ca261..0bc9fa37e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MVLikelihoodRatio.java
@@ -11,10 +11,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
index 2679a169b..96e76ceab 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityRankSumTest.java
@@ -2,12 +2,12 @@ package org.broadinstitute.sting.gatk.walkers.annotator;
 
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
index 364bbdbb9..4b11a9698 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZero.java
@@ -8,13 +8,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
index afb4ceb60..057fbaf8a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroBySample.java
@@ -31,14 +31,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
index 5f9f3416d..d0ea231a1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/MappingQualityZeroFraction.java
@@ -7,11 +7,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
index 3e6aa62a2..1aaf3afcd 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/NBaseCount.java
@@ -6,11 +6,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index d75947879..af27d9c6f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -8,11 +8,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
index 474b6b150..883e2ddce 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RMSMappingQuality.java
@@ -10,12 +10,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnota
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFStandardHeaderLines;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFStandardHeaderLines;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
index e7c0e6b14..adc661d66 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/RankSumTest.java
@@ -10,14 +10,14 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MannWhitneyU;
 import org.broadinstitute.sting.utils.QualityUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
index 334b89f01..de1fdf0d0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/ReadPosRankSumTest.java
@@ -7,14 +7,14 @@ import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
index 33e895187..090702e42 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SampleList.java
@@ -31,11 +31,11 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
index b3b0be153..a19b77aae 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SnpEff.java
@@ -35,9 +35,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
@@ -212,7 +213,7 @@ public class SnpEff extends InfoFieldAnnotation implements RodRequiringAnnotatio
 
         // Make sure that the SnpEff version number and command-line header lines are present in the VCF header of
         // the SnpEff rod, and that the file was generated by a supported version of SnpEff:
-        VCFHeader snpEffVCFHeader = VCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
+        VCFHeader snpEffVCFHeader = GATKVCFUtils.getVCFHeadersFromRods(toolkit, Arrays.asList(snpEffRodBinding.getName())).get(snpEffRodBinding.getName());
         VCFHeaderLine snpEffVersionLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_VERSION_LINE_KEY);
         VCFHeaderLine snpEffCommandLine = snpEffVCFHeader.getOtherHeaderLine(SNPEFF_VCF_HEADER_COMMAND_LINE_KEY);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
index 8e1140af1..7c113c188 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/SpanningDeletions.java
@@ -7,10 +7,10 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
index c72ba1c5f..1862ab6c6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TandemRepeatAnnotator.java
@@ -31,12 +31,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
@@ -57,7 +57,7 @@ public class TandemRepeatAnnotator extends InfoFieldAnnotation implements Standa
         if ( !vc.isIndel())
             return null;
 
-        Pair<List<Integer>,byte[]> result = VariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases());
+        Pair<List<Integer>,byte[]> result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, ref.getForwardBases());
         if (result == null)
             return null;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
index 57b50c6e2..58cce6b30 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TechnologyComposition.java
@@ -8,12 +8,12 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
index be7288a7e..40a442808 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/TransmissionDisequilibriumTest.java
@@ -10,11 +10,11 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnot
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.RodRequiringAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
index 92060b4a3..09f01bd42 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotator.java
@@ -35,13 +35,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -225,7 +226,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
         // note that if any of the definitions conflict with our new ones, then we want to overwrite the old ones
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
         hInfo.addAll(engine.getVCFAnnotationDescriptions());
-        for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
+        for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variantCollection.variants.getName())) ) {
             if ( isUniqueHeaderLine(line, hInfo) )
                 hInfo.add(line);
         }
@@ -237,7 +238,7 @@ public class VariantAnnotator extends RodWalker<Integer, Integer> implements Ann
                 continue;
             }
             VCFInfoHeaderLine targetHeaderLine = null;
-            for ( VCFHeaderLine line : VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
+            for ( VCFHeaderLine line : GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(expression.binding.getName())) ) {
                 if ( line instanceof VCFInfoHeaderLine ) {
                     VCFInfoHeaderLine infoline = (VCFInfoHeaderLine)line;
                     if ( infoline.getID().equals(expression.fieldName) ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 725097ddc..ddf5a6de1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
index a5c2b32f0..944962d30 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantType.java
@@ -8,9 +8,9 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAn
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.InfoFieldAnnotation;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.IndelUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeaderLineType;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
index 03fcba760..632b60b02 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/ActiveRegionBasedAnnotation.java
@@ -1,8 +1,8 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
index f610a2ba8..0d599332d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/AnnotatorCompatible.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
 import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
index 6970908b5..490bbdbde 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/GenotypeAnnotation.java
@@ -4,10 +4,10 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFFormatHeaderLine;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
index 5b2dc310d..ef717abd1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/InfoFieldAnnotation.java
@@ -4,8 +4,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFInfoHeaderLine;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
index 996d85a67..0ec7ef907 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/annotator/interfaces/VariantAnnotatorAnnotation.java
@@ -25,7 +25,7 @@
 package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
index 83b10dd91..bdc129b8c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCF.java
@@ -35,10 +35,11 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.beagle.BeagleFeature;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -132,7 +133,7 @@ public class BeagleOutputToVCF extends RodWalker<Integer, Integer> {
         // setup the header fields
 
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFFormatHeaderLine("OG",1, VCFHeaderLineType.String, "Original Genotype input to Beagle"));
         hInfo.add(new VCFInfoHeaderLine("R2", 1, VCFHeaderLineType.Float, "r2 Value reported by Beagle on each site"));
         hInfo.add(new VCFInfoHeaderLine("NumGenotypesChanged", 1, VCFHeaderLineType.Integer, "The number of genotypes changed by Beagle"));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
index d11747766..e02b473b6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/ProduceBeagleInput.java
@@ -38,14 +38,15 @@ import org.broadinstitute.sting.gatk.walkers.variantrecalibration.VQSRCalibratio
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFFilterHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFFilterHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.io.PrintStream;
@@ -231,7 +232,7 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
     private final static double[] DIPLOID_FLAT_LOG10_LIKELIHOODS = MathUtils.toLog10(new double[]{ 0.33, 0.33, 0.33 });
 
     public void writeBeagleOutput(VariantContext preferredVC, VariantContext otherVC, boolean isValidationSite, double prior) {
-        GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),preferredVC);
+        GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), preferredVC);
         StringBuffer beagleOut = new StringBuffer();
 
         String marker = String.format("%s:%d ",currentLoc.getContig(),currentLoc.getStart());
@@ -344,7 +345,7 @@ public class ProduceBeagleInput extends RodWalker<Integer, Integer> {
 
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
         hInfo.add(new VCFFilterHeaderLine("bootstrap","This site used for genotype bootstrapping with ProduceBeagleInputWalker"));
 
         bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames)));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
index a6a6d484e..fd552e12f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/VariantsToBeagleUnphased.java
@@ -36,16 +36,16 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.PrintStream;
 import java.util.Arrays;
@@ -90,7 +90,7 @@ public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
             throw new UserException.BadArgumentValue("bootstrap", "Bootstrap value must be fraction between 0 and 1");
 
         if ( bootstrapVCFOutput != null ) {
-            Set<VCFHeaderLine> hInfo = VCFUtils.getHeaderFields(getToolkit());
+            Set<VCFHeaderLine> hInfo = GATKVCFUtils.getHeaderFields(getToolkit());
             bootstrapVCFOutput.writeHeader(new VCFHeader(hInfo, SampleUtils.getUniqueSamplesFromRods(getToolkit())));
         }
     }
@@ -141,7 +141,7 @@ public class VariantsToBeagleUnphased extends RodWalker<Integer, Integer> {
     }
 
     public void writeUnphasedBeagleOutput(VariantContext vc, boolean makeMissing) {
-        GenomeLoc currentLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(),vc);
+        GenomeLoc currentLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc);
         StringBuffer beagleOut = new StringBuffer();
 
         String marker = String.format("%s:%d ",currentLoc.getContig(), currentLoc.getStart());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
index 4d7dbc912..f4d192373 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -38,7 +38,7 @@ import org.broadinstitute.sting.gatk.filters.*;
 import org.broadinstitute.sting.gatk.iterators.ReadTransformer;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
index 48019efea..68084e606 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CallableLoci.java
@@ -38,6 +38,7 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.variant.utils.BaseUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -305,7 +306,7 @@ public class CallableLoci extends LocusWalker<CallableLoci.CallableBaseState, Ca
     public CallableBaseState map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
         CalledState state;
 
-        if (BaseUtils.isNBase(ref.getBase())) {
+        if ( BaseUtils.isNBase(ref.getBase())) {
             state = CalledState.REF_N;
         } else {
             // count up the depths of all and QC+ bases
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
index 21532823b..85707c310 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.coverage;
 import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
index fe9942662..b1cec0e13 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverage.java
@@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
index 5345f9f48..5847471b2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageStats.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.coverage;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
index 1fe9c2e81..c75731fb7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/coverage/GCContentByInterval.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
index 471b23930..32433a5b4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
@@ -9,7 +9,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.report.GATKReport;
 import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
index cbd3bc950..095807e5c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/DiagnoseTargets.java
@@ -34,12 +34,12 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
index 0d8195551..9ebb34585 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/targets/ThresHolder.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.diagnostics.targets;
 
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
 import java.util.HashSet;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
index 5726eeed9..fe95112e7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diffengine/VCFDiffableReader.java
@@ -28,9 +28,9 @@ import org.apache.log4j.Logger;
 import org.broad.tribble.AbstractFeatureReader;
 import org.broad.tribble.FeatureReader;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.*;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.*;
 import java.util.Iterator;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
index 22c6097cf..ca605bdad 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaAlternateReferenceMaker.java
@@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Collections;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
index 6beade070..0f9b79930 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaStats.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
index 2c009f7f2..a130b8993 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/ClusteredSnps.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.filters;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 
 public class ClusteredSnps {
     private GenomeLocParser genomeLocParser;
@@ -32,7 +32,7 @@ public class ClusteredSnps {
                 throw new UserException.BadInput("The clustered SNPs filter does not work in the presence of non-variant records; see the documentation for more details");
 
             // find the nth variant
-            GenomeLoc left = VariantContextUtils.getLocation(genomeLocParser,variants[i].getVariantContext());
+            GenomeLoc left = GATKVariantContextUtils.getLocation(genomeLocParser, variants[i].getVariantContext());
             GenomeLoc right = null;
             int snpsSeen = 1;
 
@@ -40,7 +40,7 @@ public class ClusteredSnps {
             while ( ++currentIndex < variants.length ) {
                 if ( variants[currentIndex] != null && variants[currentIndex].getVariantContext() != null && variants[currentIndex].getVariantContext().isVariant() ) {
                     if ( ++snpsSeen == snpThreshold ) {
-                        right = VariantContextUtils.getLocation(genomeLocParser,variants[currentIndex].getVariantContext());
+                        right = GATKVariantContextUtils.getLocation(genomeLocParser, variants[currentIndex].getVariantContext());
                         break;
                     }
                 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
index ede19746a..676cef733 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContext.java
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.filters;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 
 public class FiltrationContext {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
index 8b3886cfb..3e0bf07e4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltration.java
@@ -37,11 +37,12 @@ import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -170,7 +171,7 @@ public class VariantFiltration extends RodWalker<Integer, Integer> {
 
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
 
         if ( clusterWindow > 0 )
             hInfo.add(new VCFFilterHeaderLine(CLUSTERED_SNP_FILTER_NAME, "SNPs found in clusters"));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
index 7dcc95361..751418a61 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/ConsensusAlleleCounter.java
@@ -36,7 +36,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
@@ -283,7 +283,7 @@ public class ConsensusAlleleCounter {
         if (vcs.isEmpty())
             return Collections.emptyList(); // nothing else to do, no alleles passed minimum count criterion
 
-        final VariantContext mergedVC = VariantContextUtils.simpleMerge(locParser, vcs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false);
+        final VariantContext mergedVC = VariantContextUtils.simpleMerge(vcs, null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED, VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, null, false, false);
         return mergedVC.getAlleles();
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
index 95b81e322..86047d30b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 
 public enum DiploidGenotype {
     AA ('A', 'A'),
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
index 2870b6629..290c33b2b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidSNPGenotypeLikelihoods.java
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
 import net.sf.samtools.SAMUtils;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
index a8ee4afde..ea09e17d8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/GenotypeLikelihoodsCalculationModel.java
@@ -30,13 +30,13 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 0d9f443e2..56965c022 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -31,14 +31,14 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Haplotype;
 import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 791cdc325..c10f7264e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
@@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
index 5f6ddf0f1..e7add3213 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
@@ -28,8 +28,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.arguments.StandardCallerArgumentCollection;
 import org.broadinstitute.sting.utils.pairhmm.PairHMM;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 public class UnifiedArgumentCollection extends StandardCallerArgumentCollection {
 
@@ -151,7 +151,7 @@ public class UnifiedArgumentCollection extends StandardCallerArgumentCollection
         Sample ploidy - equivalent to number of chromosomes per pool. In pooled experiments this should be = # of samples in pool * individual sample ploidy
      */
     @Argument(shortName="ploidy", fullName="sample_ploidy", doc="Plody (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).", required=false)
-    public int samplePloidy = VariantContextUtils.DEFAULT_PLOIDY;
+    public int samplePloidy = GATKVariantContextUtils.DEFAULT_PLOIDY;
 
     @Hidden
     @Argument(shortName="minqs", fullName="min_quality_score", doc="Min quality score to consider. Smaller numbers process faster. Default: Q1.", required=false)
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
index 36be2e7c6..7b82403b5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyper.java
@@ -42,13 +42,13 @@ import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompa
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.GATKLiteUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -232,7 +232,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
         // Check for protected modes
         if (GATKLiteUtils.isGATKLite()) {
             // no polyploid/pooled mode in GATK Like
-            if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY ||
+            if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY ||
                     UAC.referenceSampleName != null ||
                     UAC.referenceSampleRod.isBound())  {
                 throw new UserException.NotSupportedInGATKLite("you cannot enable usage of ploidy values other than 2");
@@ -303,7 +303,7 @@ public class UnifiedGenotyper extends LocusWalker<List<VariantCallContext>, Unif
             headerInfo.add(new VCFInfoHeaderLine(UnifiedGenotyperEngine.NUMBER_OF_DISCOVERED_ALLELES_KEY, 1, VCFHeaderLineType.Integer, "Number of alternate alleles discovered (but not necessarily genotyped) at this site"));
 
         // add the pool values for each genotype
-        if (UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY) {
+        if (UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY) {
             headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_COUNT_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Integer, "Maximum likelihood expectation (MLE) for the alternate allele count, in the same order as listed, for each individual sample"));
             headerInfo.add(new VCFFormatHeaderLine(VCFConstants.MLE_PER_SAMPLE_ALLELE_FRACTION_KEY, VCFHeaderLineCount.A, VCFHeaderLineType.Float, "Maximum likelihood expectation (MLE) for the alternate allele fraction, in the same order as listed, for each individual sample"));
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
index 8f2588679..1d5671857 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperEngine.java
@@ -40,11 +40,13 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.PrintStream;
 import java.lang.reflect.Constructor;
@@ -112,7 +114,7 @@ public class UnifiedGenotyperEngine {
     // ---------------------------------------------------------------------------------------------------------
     @Requires({"toolkit != null", "UAC != null"})
     public UnifiedGenotyperEngine(GenomeAnalysisEngine toolkit, UnifiedArgumentCollection UAC) {
-        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), VariantContextUtils.DEFAULT_PLOIDY);
+        this(toolkit, UAC, Logger.getLogger(UnifiedGenotyperEngine.class), null, null, SampleUtils.getSAMFileSamples(toolkit.getSAMFileHeader()), GATKVariantContextUtils.DEFAULT_PLOIDY);
     }
 
     @Requires({"toolkit != null", "UAC != null", "logger != null", "samples != null && samples.size() > 0","ploidy>0"})
@@ -503,7 +505,7 @@ public class UnifiedGenotyperEngine {
         // if we are subsetting alleles (either because there were too many or because some were not polymorphic)
         // then we may need to trim the alleles (because the original VariantContext may have had to pad at the end).
         if ( myAlleles.size() != vc.getAlleles().size() && !limitedContext ) // limitedContext callers need to handle allele trimming on their own to keep their perReadAlleleLikelihoodMap alleles in sync
-            vcCall = VariantContextUtils.reverseTrimAlleles(vcCall);
+            vcCall = GATKVariantContextUtils.reverseTrimAlleles(vcCall);
 
         if ( annotationEngine != null && !limitedContext ) { // limitedContext callers need to handle annotations on their own by calling their own annotationEngine
             // Note: we want to use the *unfiltered* and *unBAQed* context for the annotations
@@ -640,7 +642,7 @@ public class UnifiedGenotyperEngine {
     private void determineGLModelsToUse() {
 
         String modelPrefix = "";
-        if ( !UAC.GLmodel.name().contains(GPSTRING) && UAC.samplePloidy != VariantContextUtils.DEFAULT_PLOIDY )
+        if ( !UAC.GLmodel.name().contains(GPSTRING) && UAC.samplePloidy != GATKVariantContextUtils.DEFAULT_PLOIDY )
             modelPrefix = GPSTRING;
 
         if ( UAC.GLmodel.name().toUpperCase().contains("BOTH") ) {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
index 423c80112..a30ae0d34 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/VariantCallContext.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
index f783267bc..0e6c0762c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalc.java
@@ -29,9 +29,9 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.SimpleTimer;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
index 142469077..bd46c4b84 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/AFCalcResult.java
@@ -29,7 +29,7 @@ import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
index 4895c84d9..0c2e59d08 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/DiploidExactAFCalc.java
@@ -26,7 +26,8 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
@@ -84,7 +85,7 @@ public abstract class DiploidExactAFCalc extends ExactAFCalc {
             alleles.add(vc.getReference());
             alleles.addAll(chooseMostLikelyAlternateAlleles(vc, getMaxAltAlleles()));
             builder.alleles(alleles);
-            builder.genotypes(VariantContextUtils.subsetDiploidAlleles(vc, alleles, false));
+            builder.genotypes(GATKVariantContextUtils.subsetDiploidAlleles(vc, alleles, false));
             return builder.make();
         } else {
             return vc;
@@ -330,6 +331,6 @@ public abstract class DiploidExactAFCalc extends ExactAFCalc {
                                           final List<Allele> allelesToUse,
                                           final boolean assignGenotypes,
                                           final int ploidy) {
-        return VariantContextUtils.subsetDiploidAlleles(vc, allelesToUse, assignGenotypes);
+        return GATKVariantContextUtils.subsetDiploidAlleles(vc, allelesToUse, assignGenotypes);
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
index ab230d398..8e8a2d8ce 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactAFCalc.java
@@ -26,10 +26,10 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypesContext;
 
 import java.util.ArrayList;
 
@@ -71,7 +71,7 @@ abstract class ExactAFCalc extends AFCalc {
             if ( sample.hasLikelihoods() ) {
                 double[] gls = sample.getLikelihoods().getAsVector();
 
-                if ( MathUtils.sum(gls) < VariantContextUtils.SUM_GL_THRESH_NOCALL )
+                if ( MathUtils.sum(gls) < GATKVariantContextUtils.SUM_GL_THRESH_NOCALL )
                     genotypeLikelihoods.add(gls);
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
index b138ddf70..c9270a6a7 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/ExactCallLogger.java
@@ -4,7 +4,7 @@ import com.google.java.contract.Requires;
 import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.*;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
index 937ef2ffc..76017be4f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
index 67cc79646..f37e4e3d2 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/OriginalDiploidExactAFCalc.java
@@ -2,8 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
index ad6361a3f..179b5d8ba 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/StateTracker.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.genotyper.afcalc;
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
index 3a10620aa..795fc76ed 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/HaplotypeIndelErrorModel.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.Arrays;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 345f79b2b..5d19ac5e8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -54,7 +54,8 @@ import org.broadinstitute.sting.utils.sam.NWaySAMFileWriter;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index 848aaf8a3..15ced4f0b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.PrintStream;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
index b14dc9cc9..ad97e3ddc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/RealignerTargetCreator.java
@@ -41,7 +41,7 @@ import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.PrintStream;
 import java.util.ArrayList;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
index 0165c6cf3..68be1629c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetector.java
@@ -53,7 +53,7 @@ import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.refseq.RefSeqCodec;
 import org.broadinstitute.sting.utils.codecs.refseq.RefSeqFeature;
 import org.broadinstitute.sting.utils.codecs.refseq.Transcript;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.collections.CircularArray;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
@@ -64,8 +64,8 @@ import org.broadinstitute.sting.utils.interval.IntervalUtils;
 import org.broadinstitute.sting.utils.interval.OverlappingIntervalIterator;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.*;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index c629bd313..985d0a9c9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -24,8 +24,8 @@
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
index 54838b55e..e131ea5e3 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/BaseArray.java
@@ -23,7 +23,7 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 
 import java.util.Arrays;
 import java.util.LinkedList;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
index 5bbc6dacc..5515f2141 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/MergeSegregatingAlternateAllelesVCFWriter.java
@@ -28,12 +28,13 @@ import net.sf.picard.reference.ReferenceSequenceFile;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -124,7 +125,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
                 return;
         }
 
-        logger.debug("Next VC input = " + VariantContextUtils.getLocation(genomeLocParser, vc));
+        logger.debug("Next VC input = " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
         boolean curVcIsNotFiltered = vc.isNotFiltered();
 
         if (vcfrWaitingToMerge == null) {
@@ -134,20 +135,20 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
                 throw new ReviewedStingException("filteredVcfrList should be empty if not waiting to merge a vc!");
 
             if (curVcIsNotFiltered) { // still need to wait before can release vc
-                logger.debug("Waiting for new variant " + VariantContextUtils.getLocation(genomeLocParser, vc));
+                logger.debug("Waiting for new variant " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
                 vcfrWaitingToMerge = new VCFRecord(vc, false);
             }
             else if (!emitOnlyMergedRecords) { // filtered records are never merged
-                logger.debug("DIRECTLY output " + VariantContextUtils.getLocation(genomeLocParser, vc));
+                logger.debug("DIRECTLY output " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
                 innerWriter.add(vc);
             }
         }
         else { // waiting to merge vcfrWaitingToMerge
-            logger.debug("Waiting to merge " + VariantContextUtils.getLocation(genomeLocParser, vcfrWaitingToMerge.vc));
+            logger.debug("Waiting to merge " + GATKVariantContextUtils.getLocation(genomeLocParser, vcfrWaitingToMerge.vc));
 
             if (!curVcIsNotFiltered) {
                 if (!emitOnlyMergedRecords) { // filtered records are never merged
-                    logger.debug("Caching unprocessed output " + VariantContextUtils.getLocation(genomeLocParser, vc));
+                    logger.debug("Caching unprocessed output " + GATKVariantContextUtils.getLocation(genomeLocParser, vc));
                     filteredVcfrList.add(new VCFRecord(vc, false));
                 }
             }
@@ -345,10 +346,10 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
 
                         if (!PhasingUtils.alleleSegregationIsKnown(gt1, gt2)) {
                             aas.segregationUnknown++;
-                            logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + VariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + VariantContextUtils.getLocation(genomeLocParser, vc2));
+                            logger.debug("Unknown segregation of alleles [not phased] for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
                         }
                         else if (gt1.isHomRef() || gt2.isHomRef()) {
-                            logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + VariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + VariantContextUtils.getLocation(genomeLocParser, vc2));
+                            logger.debug("gt1.isHomRef() || gt2.isHomRef() for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
                             aas.eitherNotVariant++;
                         }
                         else { // BOTH gt1 and gt2 have at least one variant allele (so either hets, or homozygous variant):
@@ -377,7 +378,7 @@ class MergeSegregatingAlternateAllelesVCFWriter implements VariantContextWriter
 
                             // Check MNPs vs. CHets:
                             if (containsRefAllele(site1Alleles) && containsRefAllele(site2Alleles)) {
-                                logger.debug("HET-HET for " + samp + " at " + VariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + VariantContextUtils.getLocation(genomeLocParser, vc2));
+                                logger.debug("HET-HET for " + samp + " at " + GATKVariantContextUtils.getLocation(genomeLocParser, vc1) + ", " + GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
                                 if (logger.isDebugEnabled() && !(gt1.isHet() && gt2.isHet()))
                                     throw new ReviewedStingException("Since !gt1.isHomRef() && !gt2.isHomRef(), yet both have ref alleles, they BOTH must be hets!");
 
@@ -463,7 +464,7 @@ class DistanceMergeRule extends VariantContextMergeRule {
     }
 
     public int minDistance(VariantContext vc1, VariantContext vc2) {
-        return VariantContextUtils.getLocation(genomeLocParser, vc1).minDistance(VariantContextUtils.getLocation(genomeLocParser, vc2));
+        return GATKVariantContextUtils.getLocation(genomeLocParser, vc1).minDistance(GATKVariantContextUtils.getLocation(genomeLocParser, vc2));
     }
 }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
index 660942b5b..2b53dea43 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhaseByTransmission.java
@@ -12,11 +12,12 @@ import org.broadinstitute.sting.gatk.samples.Sample;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.PrintStream;
 import java.util.*;
@@ -396,7 +397,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
     public void initialize() {
         ArrayList<String> rodNames = new ArrayList<String>();
         rodNames.add(variantCollection.variants.getName());
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
+        Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
         Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
 
         //Get the trios from the families passed as ped
@@ -406,7 +407,7 @@ public class PhaseByTransmission extends RodWalker<HashMap<Byte,Integer>, HashMa
 
 
         Set<VCFHeaderLine> headerLines = new HashSet<VCFHeaderLine>();
-        headerLines.addAll(VCFUtils.getHeaderFields(this.getToolkit()));
+        headerLines.addAll(GATKVCFUtils.getHeaderFields(this.getToolkit()));
         headerLines.add(new VCFFormatHeaderLine(TRANSMISSION_PROBABILITY_TAG_NAME, 1, VCFHeaderLineType.Integer, "Phred score of the genotype combination and phase given that the genotypes are correct"));
         headerLines.add(new VCFHeaderLine("source", SOURCE_NAME));
         vcfWriter.writeHeader(new VCFHeader(headerLines, vcfSamples));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
index a95b13d68..4d764866d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingRead.java
@@ -23,7 +23,7 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
index 630d99ce9..5d819ccfd 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/PhasingUtils.java
@@ -29,9 +29,10 @@ import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.util.*;
 
@@ -161,8 +162,8 @@ class PhasingUtils {
     }
 
     static boolean mergeIntoMNPvalidationCheck(GenomeLocParser genomeLocParser, VariantContext vc1, VariantContext vc2) {
-        GenomeLoc loc1 = VariantContextUtils.getLocation(genomeLocParser, vc1);
-        GenomeLoc loc2 = VariantContextUtils.getLocation(genomeLocParser, vc2);
+        GenomeLoc loc1 = GATKVariantContextUtils.getLocation(genomeLocParser, vc1);
+        GenomeLoc loc2 = GATKVariantContextUtils.getLocation(genomeLocParser, vc2);
 
         if (!loc1.onSameContig(loc2))
             throw new ReviewedStingException("Can only merge vc1, vc2 if on the same chromosome");
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index 7d848d0d4..68eab9889 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -34,24 +34,26 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.filters.MappingQualityZeroFilter;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.HasGenomeLocation;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.*;
 import java.util.*;
 
-import static org.broadinstitute.sting.utils.codecs.vcf.VCFUtils.getVCFHeadersFromRods;
+import static org.broadinstitute.sting.utils.variant.GATKVCFUtils.getVCFHeadersFromRods;
 
 /**
  * Walks along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads).
@@ -212,7 +214,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
         // setup the header fields:
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit()));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit()));
         hInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
 
         // Phasing-specific INFO fields:
@@ -267,13 +269,13 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
                 unphasedSiteQueue.add(vr);
 
                 if (DEBUG)
-                    logger.debug("Added variant to queue = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant));
+                    logger.debug("Added variant to queue = " + GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant));
             }
             else {
                 unprocessedList.add(vc); // Finished with the unprocessed variant, and writer can enforce sorting on-the-fly
 
                 if (DEBUG)
-                    logger.debug("Unprocessed variant = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
+                    logger.debug("Unprocessed variant = " + GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
             }
 
             int numReads = context.getBasePileup().getNumberOfElements();
@@ -304,7 +306,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         while (!unphasedSiteQueue.isEmpty()) {
             if (!processAll) { // otherwise, phase until the end of unphasedSiteQueue
                 VariantContext nextToPhaseVc = unphasedSiteQueue.peek().variant;
-                if (startDistancesAreInWindowRange(mostDownstreamLocusReached, VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), nextToPhaseVc))) {
+                if (startDistancesAreInWindowRange(mostDownstreamLocusReached, GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), nextToPhaseVc))) {
                     /* mostDownstreamLocusReached is still not far enough ahead of nextToPhaseVc to have all phasing information for nextToPhaseVc
                      (note that we ASSUME that the VCF is ordered by <contig,locus>).
                       Note that this will always leave at least one entry (the last one), since mostDownstreamLocusReached is in range of itself.
@@ -319,7 +321,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
             VariantAndReads vr = unphasedSiteQueue.remove();
             if (DEBUG)
-                logger.debug("Performing phasing for " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant));
+                logger.debug("Performing phasing for " + GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant));
             phaseSite(vr, phaseStats);
         }
 
@@ -338,7 +340,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
         GenomeLoc nextToPhaseLoc = null;
         if (!unphasedSiteQueue.isEmpty())
-            nextToPhaseLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), unphasedSiteQueue.peek().variant);
+            nextToPhaseLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), unphasedSiteQueue.peek().variant);
 
         while (!partiallyPhasedSites.isEmpty()) {
             if (nextToPhaseLoc != null) { // otherwise, unphasedSiteQueue.isEmpty(), and therefore no need to keep any of the "past"
@@ -363,7 +365,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
     private void phaseSite(VariantAndReads vr, PhasingStats phaseStats) {
         VariantContext vc = vr.variant;
-        logger.debug("Will phase vc = " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
+        logger.debug("Will phase vc = " + GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
 
         UnfinishedVariantAndReads uvr = new UnfinishedVariantAndReads(vr);
         UnfinishedVariantContext uvc = uvr.unfinishedVariant;
@@ -400,7 +402,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
 
                         if (pr.phasingContainsInconsistencies) {
                             if (DEBUG)
-                                logger.debug("MORE than " + (MAX_FRACTION_OF_INCONSISTENT_READS * 100) + "% of the reads are inconsistent for phasing of " + VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
+                                logger.debug("MORE than " + (MAX_FRACTION_OF_INCONSISTENT_READS * 100) + "% of the reads are inconsistent for phasing of " + GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
                             uvc.setPhasingInconsistent();
                         }
 
@@ -441,7 +443,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
                         }
 
                         if (statsWriter != null)
-                            statsWriter.addStat(samp, VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc), startDistance(prevUvc, vc), pr.phaseQuality, phaseWindow.readsAtHetSites.size(), phaseWindow.hetGenotypes.length);
+                            statsWriter.addStat(samp, GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc), startDistance(prevUvc, vc), pr.phaseQuality, phaseWindow.readsAtHetSites.size(), phaseWindow.hetGenotypes.length);
 
                         PhaseCounts sampPhaseCounts = samplePhaseStats.get(samp);
                         if (sampPhaseCounts == null) {
@@ -538,7 +540,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
             }
 
             // Add the (het) position to be phased:
-            GenomeLoc phaseLocus = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant);
+            GenomeLoc phaseLocus = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vr.variant);
             GenotypeAndReadBases grbPhase = new GenotypeAndReadBases(vr.variant.getGenotype(sample), vr.sampleReadBases.get(sample), phaseLocus);
             listHetGenotypes.add(grbPhase);
             if (DEBUG)
@@ -553,7 +555,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
                     break;
                 }
                 else if (gt.isHet()) {
-                    GenotypeAndReadBases grb = new GenotypeAndReadBases(gt, nextVr.sampleReadBases.get(sample), VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), nextVr.variant));
+                    GenotypeAndReadBases grb = new GenotypeAndReadBases(gt, nextVr.sampleReadBases.get(sample), GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), nextVr.variant));
                     listHetGenotypes.add(grb);
                     if (DEBUG) logger.debug("Using DOWNSTREAM het site = " + grb.loc);
                 }
@@ -1027,7 +1029,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
     }
 
     private boolean startDistancesAreInWindowRange(VariantContext vc1, VariantContext vc2) {
-        return startDistancesAreInWindowRange(VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc1), VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc2));
+        return startDistancesAreInWindowRange(GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc1), GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc2));
     }
 
     private boolean startDistancesAreInWindowRange(GenomeLoc loc1, GenomeLoc loc2) {
@@ -1035,7 +1037,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
     }
 
     private int startDistance(UnfinishedVariantContext uvc1, VariantContext vc2) {
-        return uvc1.getLocation().distance(VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc2));
+        return uvc1.getLocation().distance(GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc2));
     }
 
     public PhasingStats reduce(PhasingStatsAndOutput statsAndList, PhasingStats stats) {
@@ -1219,7 +1221,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
             else
                 sb.append(" -- ");
 
-            sb.append(VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
+            sb.append(GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), vc));
         }
         return sb.toString();
     }
@@ -1475,7 +1477,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
         public void outputMultipleBaseCounts() {
             GenomeLoc nextToPhaseLoc = null;
             if (!unphasedSiteQueue.isEmpty())
-                nextToPhaseLoc = VariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), unphasedSiteQueue.peek().variant);
+                nextToPhaseLoc = GATKVariantContextUtils.getLocation(getToolkit().getGenomeLocParser(), unphasedSiteQueue.peek().variant);
 
             outputMultipleBaseCounts(nextToPhaseLoc);
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
index 6a2381e29..064a3b452 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/SNPallelePair.java
@@ -23,10 +23,10 @@
  */
 package org.broadinstitute.sting.gatk.walkers.phasing;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
 
 class SNPallelePair extends AllelePair {
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
index 5e3f5b038..254a5422b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/DocumentationTest.java
@@ -32,8 +32,8 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
index 5082645ad..412ee48aa 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/QCRef.java
@@ -32,7 +32,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RefWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
index 4e67beffe..9d4f948a8 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/qc/RodSystemValidation.java
@@ -25,7 +25,6 @@
 package org.broadinstitute.sting.gatk.walkers.qc;
 
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
@@ -35,8 +34,7 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.*;
 import java.math.BigInteger;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
index 79b6e17f6..f889a8c76 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/GenotypeAndValidate.java
@@ -36,14 +36,15 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.vcf.VCFUtils;
 
 import java.util.Map;
 import java.util.Set;
@@ -304,7 +305,7 @@ public class GenotypeAndValidate extends RodWalker<GenotypeAndValidate.CountedDa
 
         // Initialize VCF header
         if (vcfWriter != null) {
-            Map<String, VCFHeader> header = VCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
+            Map<String, VCFHeader> header = GATKVCFUtils.getVCFHeadersFromRodPrefix(getToolkit(), alleles.getName());
             samples = SampleUtils.getSampleList(header, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
             Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(header.values(), logger);
             headerLines.add(new VCFHeaderLine("source", "GenotypeAndValidate"));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
index 9d96dedef..aaab1af83 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/ValidationAmplicons.java
@@ -16,11 +16,11 @@ import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.PrintStream;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
index 62305d3c0..6bd0cbc4b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/FrequencyModeSelector.java
@@ -24,12 +24,9 @@
 package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
-import java.util.HashMap;
 
 public abstract class FrequencyModeSelector  implements Cloneable{
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
index d71d0c9c8..6d7f2b672 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GLBasedSampleSelector.java
@@ -26,7 +26,7 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalc;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcFactory;
 import org.broadinstitute.sting.gatk.walkers.genotyper.afcalc.AFCalcResult;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.TreeSet;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
index de832b108..c69325d00 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GTBasedSampleSelector.java
@@ -24,12 +24,8 @@
 
 package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.ArrayList;
-import java.util.Map;
-import java.util.Set;
 import java.util.TreeSet;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
index 67ddc47ff..c4c9b0e9d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/GenomeEvent.java
@@ -27,9 +27,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 
 import java.util.HashMap;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
index 7c1d63f02..a259544ca 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/KeepAFSpectrumFrequencySelector.java
@@ -26,9 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
index a48bcb8a1..0a3ae538a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/NullSampleSelector.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import java.util.TreeSet;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
index afbff93d0..2632716a9 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/SampleSelector.java
@@ -23,7 +23,7 @@
  */
 package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import java.util.TreeSet;
 
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
index 4019c5631..7d03e8edb 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/UniformSamplingFrequencySelector.java
@@ -25,9 +25,9 @@ package org.broadinstitute.sting.gatk.walkers.validation.validationsiteselector;
 
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
index 9e5fd25a9..8a3efb50d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/validation/validationsiteselector/ValidationSiteSelector.java
@@ -31,13 +31,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.util.*;
@@ -203,7 +203,7 @@ public class ValidationSiteSelector extends RodWalker<Integer, Integer> {
 
     public void initialize() {
          // Get list of samples to include in the output
-         Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
+         Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
          TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
 
          Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
index 201028d99..dc0f8f3fe 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEval.java
@@ -23,15 +23,16 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatc
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.VariantEvalUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -172,7 +173,7 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
     protected double MENDELIAN_VIOLATION_QUAL_THRESHOLD = 50;
 
     @Argument(shortName="ploidy", fullName="samplePloidy", doc="Per-sample ploidy (number of chromosomes per sample)", required=false)
-    protected int ploidy = VariantContextUtils.DEFAULT_PLOIDY;
+    protected int ploidy = GATKVariantContextUtils.DEFAULT_PLOIDY;
 
     @Argument(fullName="ancestralAlignments", shortName="aa", doc="Fasta file with ancestral alleles", required=false)
     private File ancestralAlignmentsFile = null;
@@ -259,7 +260,7 @@ public class VariantEval extends RodWalker<Integer, Integer> implements TreeRedu
         }
 
         // Now that we have all the rods categorized, determine the sample list from the eval rods.
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), evals);
+        Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), evals);
         Set<String> vcfSamples = SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE);
 
         // Load the sample list, using an intermediate tree set to sort the samples
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
index c14754715..be1e300e2 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
@@ -5,8 +5,8 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * The Broad Institute
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
index c7392cff0..3d5d5415c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CountVariants.java
@@ -6,8 +6,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 @Analysis(description = "Counts different classes of variants in the sample")
 public class CountVariants extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
index 15f791e9d..e51068431 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypeConcordance.java
@@ -7,9 +7,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeType;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeType;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
index 0b17c7adb..2cfade223 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelLengthHistogram.java
@@ -30,8 +30,8 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Molten;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
index dda7e8611..fc2e205c6 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/IndelSummary.java
@@ -32,9 +32,9 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 @Analysis(description = "Evaluation summary for indels")
 public class IndelSummary extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
index 97a8b4dda..755fd1b03 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MendelianViolationEvaluator.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.MendelianViolation;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Map;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
index 09c8687eb..f0b4dd90d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/MultiallelicSummary.java
@@ -31,9 +31,9 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 @Analysis(description = "Evaluation summary for multi-allelic variants")
 public class MultiallelicSummary extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
index a0cb662e0..b1ec79586 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/PrintMissingComp.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 @Analysis(name = "PrintMissingComp", description = "the overlap between eval and comp sites")
 public class PrintMissingComp extends VariantEvaluator {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
index b87a8ee85..091eed217 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ThetaVariantEvaluator.java
@@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.concurrent.ConcurrentHashMap;
 import java.util.concurrent.ConcurrentMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
index fe2437976..f761ce973 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/TiTvVariantEvaluator.java
@@ -5,9 +5,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 @Analysis(description = "Ti/Tv Variant Evaluator")
 public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEval {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
index a2bcdaf1d..323e67c75 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/ValidationReport.java
@@ -5,10 +5,10 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Collection;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
index c08ff379b..162ca5df1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantEvaluator.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 public abstract class VariantEvaluator implements Comparable<VariantEvaluator> {
     private VariantEval walker;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
index 71ea6af98..151fb8fa5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/VariantSummary.java
@@ -34,11 +34,11 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java
index 500ab8e65..9845318a0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/genotypePhasingEvaluator/GenotypePhasingEvaluator.java
@@ -13,9 +13,9 @@
 //import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext;
 //import org.broadinstitute.sting.utils.GenomeLoc;
 //import org.broadinstitute.sting.utils.MathUtils;
-//import org.broadinstitute.sting.utils.variantcontext.Genotype;
-//import org.broadinstitute.sting.utils.variantcontext.GenotypesContext;
-//import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+//import org.broadinstitute.variant.variantcontext.Genotype;
+//import org.broadinstitute.variant.variantcontext.GenotypesContext;
+//import org.broadinstitute.variant.variantcontext.VariantContext;
 //
 //import java.util.HashMap;
 //import java.util.HashSet;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
index 7197fc14c..51552d552 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleCount.java
@@ -4,10 +4,10 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
index 817663026..f35b33c47 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/AlleleFrequency.java
@@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
index 1274028d7..425aca43c 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CompRod.java
@@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
index 328bab1db..b1b8d53a1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Contig.java
@@ -2,9 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
index 7536b0237..97aa45773 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/CpG.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
index eab59864f..ceefb8e43 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Degeneracy.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.HashMap;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java
index 21255f7b3..d4646a3ce 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/DynamicStratification.java
@@ -24,11 +24,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * Tag this stratification as dynamically determining the final strat based on the input data
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
index 6328d6a51..5aa47a0a5 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/EvalRod.java
@@ -3,9 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
index 278ced713..72e3e2838 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Filter.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
index 330451fff..2ebe49228 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/FunctionalClass.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.SnpEff;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
index 089351eaa..6bb738f7e 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IndelSize.java
@@ -2,9 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
index 4fc381b3f..bbb9ef9f4 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/IntervalStratification.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
index c89c4be66..d152b086e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/JexlExpression.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.SortableJexlVCMatchExp;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.List;
 import java.util.ArrayList;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
index 2ad08d806..61bc3f0b4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Novelty.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
index 65633bc2b..7ffc3f56b 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/OneBPIndel.java
@@ -26,10 +26,9 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
-import java.util.Collections;
 import java.util.List;
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
index 621f4337f..62f5282c7 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/Sample.java
@@ -4,7 +4,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantSummary;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
index 834c02b83..aaa8e685a 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/TandemRepeat.java
@@ -24,11 +24,10 @@
 
 package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
-import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.List;
@@ -51,7 +50,7 @@ public class TandemRepeat extends VariantStratifier {
     public List<Object> getRelevantStates(ReferenceContext ref, RefMetaDataTracker tracker, VariantContext comp, String compName, VariantContext eval, String evalName, String sampleName) {
         if ( eval == null || ! eval.isIndel() )
             return ALL;
-        else if ( VariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) {
+        else if ( GATKVariantContextUtils.isTandemRepeat(eval, ref.getForwardBases()) ) {
             print("REPEAT", eval, ref);
             return REPEAT;
         } else {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
index 90b6230ca..ffaa00b4a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantStratifier.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.Stratifier;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Collections;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
index 09b89386f..081d09ded 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/stratifications/VariantType.java
@@ -26,9 +26,8 @@ package org.broadinstitute.sting.gatk.walkers.varianteval.stratifications;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
-import java.util.Arrays;
 import java.util.Collections;
 import java.util.List;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
index c98c05a9a..07eb3ee7a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/EvaluationContext.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEval;
 import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Set;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
index 38f7a7f40..737c49e43 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/SortableJexlVCMatchExp.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.walkers.varianteval.util;
 
 import org.apache.commons.jexl2.Expression;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 public class SortableJexlVCMatchExp extends VariantContextUtils.JexlVCMatchExp implements Comparable<SortableJexlVCMatchExp> {
     /**
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
index e84b0b10e..3d22b7665 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/util/VariantEvalUtils.java
@@ -35,12 +35,12 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Require
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.StandardStratification;
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.VariantStratifier;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 158d1e78a..dbe6ce9e1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -38,12 +38,13 @@ import org.broadinstitute.sting.gatk.walkers.PartitionType;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.util.*;
@@ -150,7 +151,7 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
 
         // setup the header fields
         final Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
         addVQSRStandardHeaderLines(hInfo);
         final TreeSet<String> samples = new TreeSet<String>();
         samples.addAll(SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
index 5f688d001..a177ce904 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/TrainingSet.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.commandline.RodBinding;
 import org.broadinstitute.sting.commandline.Tags;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * Created by IntelliJ IDEA.
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
index 04ba3ff14..361677e37 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VQSRCalibrationCurve.java
@@ -29,7 +29,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
index f18db412f..016ce7372 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
@@ -30,15 +30,15 @@ import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.help.HelpUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index c670ad2fd..bdbcb8399 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -38,15 +38,15 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.R.RScriptExecutor;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.io.Resource;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.io.FileNotFoundException;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 68fac7631..eb671ff4a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -37,14 +37,15 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.gatk.walkers.annotator.ChromosomeCounts;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.Options;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.Options;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.util.*;
 
@@ -192,7 +193,7 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
     private Set<String> samples;
 
     public void initialize() {
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit());
+        Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
 
         if ( vcfWriter instanceof VariantContextWriterStub) {
             sitesOnlyVCF = ((VariantContextWriterStub)vcfWriter).getWriterOptions().contains(Options.DO_NOT_WRITE_GENOTYPES);
@@ -289,13 +290,13 @@ public class CombineVariants extends RodWalker<Integer, Integer> implements Tree
             // iterate over the types so that it's deterministic
             for (VariantContext.Type type : VariantContext.Type.values()) {
                 if (VCsByType.containsKey(type))
-                    mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
+                    mergedVCs.add(VariantContextUtils.simpleMerge(VCsByType.get(type),
                             priority, rodNames.size() , filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
                             SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
             }
         }
         else if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) {
-            mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcs,
+            mergedVCs.add(VariantContextUtils.simpleMerge(vcs,
                     priority, rodNames.size(), filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
                     SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
index 92d6e686b..055e73b5a 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/FilterLiftedVariants.java
@@ -33,12 +33,12 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
@@ -62,7 +62,7 @@ public class FilterLiftedVariants extends RodWalker<Integer, Integer> {
     public void initialize() {
         String trackName = variantCollection.variants.getName();
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
-        Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
+        Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
         final VCFHeader vcfHeader = new VCFHeader(vcfHeaders.containsKey(trackName) ? vcfHeaders.get(trackName).getMetaDataInSortedOrder() : Collections.<VCFHeaderLine>emptySet(), samples);
         writer.writeHeader(vcfHeader);
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
index 9fe499a03..fbb81fda0 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
@@ -39,14 +39,14 @@ import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.util.*;
 
@@ -93,7 +93,7 @@ public class LeftAlignVariants extends RodWalker<Integer, Integer> {
     public void initialize() {
         String trackName = variantCollection.variants.getName();
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
-        Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
+        Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
         Set<VCFHeaderLine> headerLines = vcfHeaders.get(trackName).getMetaDataInSortedOrder();
         baseWriter.writeHeader(new VCFHeader(headerLines, samples));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
index 63209e98c..0afa4e46e 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LiftoverVariants.java
@@ -38,14 +38,15 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.File;
 import java.util.*;
@@ -94,7 +95,7 @@ public class LiftoverVariants extends RodWalker<Integer, Integer> {
 
         String trackName = variantCollection.variants.getName();
         Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName));
-        Map<String, VCFHeader> vcfHeaders = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
+        Map<String, VCFHeader> vcfHeaders = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList(trackName));
 
         Set<VCFHeaderLine> metaData = new HashSet<VCFHeaderLine>();
         if ( vcfHeaders.containsKey(trackName) )
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
index 2ab5136a7..2d8f9df8f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/RandomlySplitVariants.java
@@ -35,14 +35,14 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.File;
 import java.util.*;
@@ -78,7 +78,7 @@ public class RandomlySplitVariants extends RodWalker<Integer, Integer> {
         final List<String> inputNames = Arrays.asList(variantCollection.variants.getName());
         Set<String> samples = SampleUtils.getUniqueSamplesFromRods(getToolkit(), inputNames);
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
 
         vcfWriter1.writeHeader(new VCFHeader(hInfo, samples));
         vcfWriter2 = VariantContextWriterFactory.create(file2, getMasterSequenceDictionary());
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
index 46a3a8cd1..f9453e7c4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectHeaders.java
@@ -35,12 +35,13 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.broadinstitute.sting.utils.text.ListFileUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.util.*;
@@ -148,7 +149,7 @@ public class SelectHeaders extends RodWalker<Integer, Integer> implements TreeRe
         // Get list of samples to include in the output
         List<String> rodNames = Arrays.asList(variantCollection.variants.getName());
 
-        Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
+        Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
         Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), logger);
 
         headerLines.add(new VCFHeaderLine(VCFHeader.SOURCE_KEY, "SelectHeaders"));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 9253446c8..cffd405b1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -41,12 +41,14 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.utils.MendelianViolation;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -349,7 +351,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
         // Get list of samples to include in the output
         List<String> rodNames = Arrays.asList(variantCollection.variants.getName());
 
-        vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
+        vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), rodNames);
         TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
 
         Collection<String> samplesFromFile = SampleUtils.getSamplesFromFiles(sampleFiles);
@@ -451,7 +453,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
             UAC.GLmodel = GenotypeLikelihoodsCalculationModel.Model.BOTH;
             UAC.OutputMode = UnifiedGenotyperEngine.OUTPUT_MODE.EMIT_ALL_SITES;
             UAC.GenotypingMode = GenotypeLikelihoodsCalculationModel.GENOTYPING_MODE.GENOTYPE_GIVEN_ALLELES;
-            UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, VariantContextUtils.DEFAULT_PLOIDY);
+            UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples, GATKVariantContextUtils.DEFAULT_PLOIDY);
             headerLines.addAll(UnifiedGenotyper.getHeaderInfo(UAC, null, null));
         }
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
index 189772f01..8e42f803b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/ValidateVariants.java
@@ -34,11 +34,11 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
index 9236247f1..dfc9a8eea 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantValidationAssessor.java
@@ -34,13 +34,14 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.util.*;
 
@@ -164,7 +165,7 @@ public class VariantValidationAssessor extends RodWalker<VariantContext,Integer>
 
         // setup the header fields
         Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-        hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), inputNames));
+        hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), inputNames));
 
         // set up the info and filter headers
         hInfo.add(new VCFInfoHeaderLine("NoCallPct", 1, VCFHeaderLineType.Float, "Percent of no-calls"));
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
index 4777b807f..98fe6636c 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToBinaryPed.java
@@ -1,7 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.alignment.bwa.java.AlignmentMatchSequence;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.arguments.DbsnpArgumentCollection;
@@ -10,18 +9,16 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Reference;
-import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.*;
 import java.util.*;
@@ -117,7 +114,7 @@ public class VariantsToBinaryPed extends RodWalker<Integer,Integer> {
         // family ID, individual ID, Paternal ID, Maternal ID, Sex, Phenotype
         int dummyID = 0; // increments for dummy parental and family IDs used
         // want to be especially careful to maintain order here
-        Map<String,VCFHeader> headers = VCFUtils.getVCFHeadersFromRods(getToolkit());
+        Map<String,VCFHeader> headers = GATKVCFUtils.getVCFHeadersFromRods(getToolkit());
         for ( Map.Entry<String,VCFHeader> header : headers.entrySet() ) {
             if ( ! header.getKey().equals(variantCollection.variants.getName()) && ! metaDataFile.getAbsolutePath().endsWith(".fam") ) {
                 continue;
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
index dd5264a1b..ff65197b1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToTable.java
@@ -27,19 +27,19 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.utils.SampleUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.io.PrintStream;
 import java.lang.reflect.Array;
@@ -178,7 +178,7 @@ public class VariantsToTable extends RodWalker<Integer, Integer> {
     public void initialize() {
 
         if ( !genotypeFieldsToTake.isEmpty() ) {
-            Map<String, VCFHeader> vcfRods = VCFUtils.getVCFHeadersFromRods(getToolkit(), variants);
+            Map<String, VCFHeader> vcfRods = GATKVCFUtils.getVCFHeadersFromRods(getToolkit(), variants);
             TreeSet<String> vcfSamples = new TreeSet<String>(SampleUtils.getSampleList(vcfRods, VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
             samples.addAll(vcfSamples);
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
index 059e9c5fb..7c44966d8 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
@@ -39,16 +39,17 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.Reference;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.SampleUtils;
 import org.broadinstitute.sting.utils.codecs.hapmap.RawHapMapFeature;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
-import org.broadinstitute.sting.utils.variantcontext.*;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.File;
 import java.util.*;
@@ -212,7 +213,7 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
 
             // setup the header fields
             Set<VCFHeaderLine> hInfo = new HashSet<VCFHeaderLine>();
-            hInfo.addAll(VCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
+            hInfo.addAll(GATKVCFUtils.getHeaderFields(getToolkit(), Arrays.asList(variants.getName())));
             hInfo.add(VCFStandardHeaderLines.getFormatLine(VCFConstants.GENOTYPE_KEY));
 
             allowedGenotypeFormatStrings.add(VCFConstants.GENOTYPE_KEY);
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
index 2226c6458..597a916f1 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentDefinitionField.java
@@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter;
 import org.broad.tribble.Tribble;
 import org.broadinstitute.sting.commandline.*;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.lang.annotation.Annotation;
diff --git a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
index 108a1c423..54eb67d8c 100644
--- a/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
+++ b/public/java/src/org/broadinstitute/sting/queue/extensions/gatk/ArgumentField.java
@@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileWriter;
 import org.apache.commons.lang.StringEscapeUtils;
 import org.apache.commons.lang.StringUtils;
 import org.broadinstitute.sting.gatk.filters.PlatformUnitFilterHelper;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 
 import java.io.File;
 import java.io.InputStream;
diff --git a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index bf60b4a80..dbffacfbc 100644
--- a/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/public/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -34,10 +34,10 @@ import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * Factory class for creating GenomeLocs
diff --git a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
index 4c708f2bf..2476a666e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
+++ b/public/java/src/org/broadinstitute/sting/utils/Haplotype.java
@@ -24,15 +24,14 @@
 
 package org.broadinstitute.sting.utils;
 
-import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.Cigar;
 import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.Serializable;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
index 9b1cc9733..8601f08b4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/IndelUtils.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.ArrayList;
 import java.util.Arrays;
diff --git a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
index a605a5596..ed55d2f97 100755
--- a/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
+++ b/public/java/src/org/broadinstitute/sting/utils/MendelianViolation.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.gatk.samples.Sample;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeType;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.GenotypeType;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
index 26c95bffd..2ccc145f9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/SampleUtils.java
@@ -28,12 +28,12 @@ package org.broadinstitute.sting.utils;
 import net.sf.samtools.SAMFileHeader;
 import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
+import org.broadinstitute.sting.utils.variant.GATKVCFUtils;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.text.ListFileUtils;
 import org.broadinstitute.sting.utils.text.XReadLines;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.variant.variantcontext.VariantContextUtils;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -102,18 +102,18 @@ public class SampleUtils {
     public static Set<String> getUniqueSamplesFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
         Set<String> samples = new LinkedHashSet<String>();
 
-        for ( VCFHeader header : VCFUtils.getVCFHeadersFromRods(toolkit, rodNames).values() )
+        for ( VCFHeader header : GATKVCFUtils.getVCFHeadersFromRods(toolkit, rodNames).values() )
             samples.addAll(header.getGenotypeSamples());
 
         return samples;
     }
 
     public static Set<String> getRodNamesWithVCFHeader(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
-        return VCFUtils.getVCFHeadersFromRods(toolkit, rodNames).keySet();
+        return GATKVCFUtils.getVCFHeadersFromRods(toolkit, rodNames).keySet();
     }
 
     public static Set<String> getSampleListWithVCFHeader(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
-        return getSampleList(VCFUtils.getVCFHeadersFromRods(toolkit, rodNames));
+        return getSampleList(GATKVCFUtils.getVCFHeadersFromRods(toolkit, rodNames));
     }
 
     public static Set<String> getSampleList(Map<String, VCFHeader> headers) {
@@ -149,7 +149,7 @@ public class SampleUtils {
 
         // iterate to get all of the sample names
 
-        for ( Map.Entry<String, VCFHeader> pair : VCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) {
+        for ( Map.Entry<String, VCFHeader> pair : GATKVCFUtils.getVCFHeadersFromRods(toolkit).entrySet() ) {
             for ( String sample : pair.getValue().getGenotypeSamples() )
                 addUniqueSample(samples, sampleOverlapMap, rodNamesToSampleNames, sample, pair.getKey());
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
index 0aa9ecba2..fc7df9f76 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/beagle/BeagleFeature.java
@@ -25,7 +25,7 @@
 package org.broadinstitute.sting.utils.codecs.beagle;
 
 import org.broad.tribble.Feature;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.ArrayList;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java
index d0480a90b..2a36e8ad3 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java
+++ b/public/java/src/org/broadinstitute/sting/utils/codecs/hapmap/RawHapMapFeature.java
@@ -26,7 +26,7 @@ package org.broadinstitute.sting.utils.codecs.hapmap;
 
 import org.broad.tribble.Feature;
 import org.broad.tribble.annotation.Strand;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.HashMap;
 import java.util.Map;
diff --git a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
index 7ae575534..85e4a338a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.utils.duplicates;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.QualityUtils;
diff --git a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index 523fd5a97..b1410da27 100755
--- a/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/public/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -32,7 +32,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.help.DocumentedGATKFeature;
 import org.broadinstitute.sting.utils.help.HelpUtils;
 import org.broadinstitute.sting.utils.sam.ReadUtils;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
index 9bb0e646f..10d35684b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/PerReadAlleleLikelihoodMap.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.PrintStream;
 import java.lang.reflect.Constructor;
diff --git a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
index 7db818592..1a27c6ecb 100644
--- a/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
+++ b/public/java/src/org/broadinstitute/sting/utils/genotyper/StandardPerReadAlleleLikelihoodMap.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.utils.genotyper;
 import org.broadinstitute.sting.utils.classloader.PublicPackageSource;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.io.PrintStream;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index ff274499b..7f323adae 100644
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -25,7 +25,7 @@
 package org.broadinstitute.sting.utils.pileup;
 
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.fragments.FragmentCollection;
diff --git a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
index 8cba5ec23..429de4a0f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
+++ b/public/java/src/org/broadinstitute/sting/utils/pileup/PileupElement.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.pileup;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
index 7e90d98b9..48b367ea7 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/RecalUtils.java
@@ -31,7 +31,7 @@ import org.broadinstitute.sting.gatk.report.GATKReportTable;
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.recalibration.covariates.*;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.R.RScriptExecutor;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
index b586a1607..6619c24eb 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/ContextCovariate.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates;
 
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.clipping.ClippingRepresentation;
 import org.broadinstitute.sting.utils.clipping.ReadClipper;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
index a9b6c7152..6bff833e4 100755
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/CycleCovariate.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.recalibration.covariates;
 
 import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.NGSPlatform;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
diff --git a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
index d4e4ab65e..36352f806 100644
--- a/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
+++ b/public/java/src/org/broadinstitute/sting/utils/recalibration/covariates/RepeatLengthCovariate.java
@@ -1,11 +1,9 @@
 package org.broadinstitute.sting.utils.recalibration.covariates;
 
 import org.broadinstitute.sting.gatk.walkers.bqsr.RecalibrationArgumentCollection;
-import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.TandemRepeat;
-import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.recalibration.ReadCovariates;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 
 import java.util.Arrays;
 
@@ -29,9 +27,9 @@ public class RepeatLengthCovariate implements ExperimentalCovariate {
             int maxRL = 0;
             for (int str = 1; str <= 8; str++) {
                 if (i + str <= readBytes.length) {
-                    maxRL = Math.max(maxRL, VariantContextUtils.findNumberofRepetitions(
-                            Arrays.copyOfRange(readBytes,i,i + str),
-                            Arrays.copyOfRange(readBytes,i,readBytes.length)
+                    maxRL = Math.max(maxRL, GATKVariantContextUtils.findNumberofRepetitions(
+                            Arrays.copyOfRange(readBytes, i, i + str),
+                            Arrays.copyOfRange(readBytes, i, readBytes.length)
                     ));
                 }
             }
diff --git a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 585578958..7ef05edd8 100644
--- a/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -30,7 +30,7 @@ import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
new file mode 100755
index 000000000..4e394ace5
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVCFUtils.java
@@ -0,0 +1,178 @@
+/*
+ * Copyright (c) 2010 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
+ * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.utils.variant;
+
+import org.broad.tribble.Feature;
+import org.broad.tribble.FeatureCodecHeader;
+import org.broad.tribble.readers.PositionalBufferedStream;
+import org.broadinstitute.sting.commandline.RodBinding;
+import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
+import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.*;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.util.*;
+
+/**
+ * A set of GATK-specific static utility methods for common operations on VCF files/records.
+ */
+public class GATKVCFUtils {
+
+    /**
+     * Constructor access disallowed...static utility methods only!
+     */
+    private GATKVCFUtils() { }
+
+    public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
+        // Collect the eval rod names
+        final Set<String> names = new TreeSet<String>();
+        for ( final RodBinding<T> evalRod : rodBindings )
+            names.add(evalRod.getName());
+        return getVCFHeadersFromRods(toolkit, names);
+    }
+
+    public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) {
+        return getVCFHeadersFromRods(toolkit, (Collection<String>)null);
+    }
+
+    public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
+        Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
+
+        // iterate to get all of the sample names
+        List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
+        for ( ReferenceOrderedDataSource source : dataSources ) {
+            // ignore the rod if it's not in our list
+            if ( rodNames != null && !rodNames.contains(source.getName()) )
+                continue;
+
+            if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader )
+                data.put(source.getName(), (VCFHeader)source.getHeader());
+        }
+
+        return data;
+    }
+
+    public static Map<String,VCFHeader> getVCFHeadersFromRodPrefix(GenomeAnalysisEngine toolkit,String prefix) {
+        Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
+
+        // iterate to get all of the sample names
+        List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
+        for ( ReferenceOrderedDataSource source : dataSources ) {
+            // ignore the rod if lacks the prefix
+            if ( ! source.getName().startsWith(prefix) )
+                continue;
+
+            if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader )
+                data.put(source.getName(), (VCFHeader)source.getHeader());
+        }
+
+        return data;
+    }
+
+    /**
+     * Gets the header fields from all VCF rods input by the user
+     *
+     * @param toolkit    GATK engine
+     *
+     * @return a set of all fields
+     */
+    public static Set<VCFHeaderLine> getHeaderFields(GenomeAnalysisEngine toolkit) {
+        return getHeaderFields(toolkit, null);
+    }
+
+    /**
+     * Gets the header fields from all VCF rods input by the user
+     *
+     * @param toolkit    GATK engine
+     * @param rodNames   names of rods to use, or null if we should use all possible ones
+     *
+     * @return a set of all fields
+     */
+    public static Set<VCFHeaderLine> getHeaderFields(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
+
+        // keep a map of sample name to occurrences encountered
+        TreeSet<VCFHeaderLine> fields = new TreeSet<VCFHeaderLine>();
+
+        // iterate to get all of the sample names
+        List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
+        for ( ReferenceOrderedDataSource source : dataSources ) {
+            // ignore the rod if it's not in our list
+            if ( rodNames != null && !rodNames.contains(source.getName()) )
+                continue;
+
+            if ( source.getRecordType().equals(VariantContext.class)) {
+                VCFHeader header = (VCFHeader)source.getHeader();
+                if ( header != null )
+                    fields.addAll(header.getMetaDataInSortedOrder());
+            }
+        }
+
+        return fields;
+    }
+
+    /**
+     * Add / replace the contig header lines in the VCFHeader with the information in the GATK engine
+     *
+     * @param header the header to update
+     * @param engine the GATK engine containing command line arguments and the master sequence dictionary
+     */
+    public static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) {
+        return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary());
+    }
+
+    /**
+     * Read all of the VCF records from source into memory, returning the header and the VariantContexts
+     *
+     * @param source the file to read, must be in VCF4 format
+     * @return
+     * @throws java.io.IOException
+     */
+    public static Pair<VCFHeader, List<VariantContext>> readVCF(final File source) throws IOException {
+        // read in the features
+        final List<VariantContext> vcs = new ArrayList<VariantContext>();
+        final VCFCodec codec = new VCFCodec();
+        PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
+        FeatureCodecHeader header = codec.readHeader(pbs);
+        pbs.close();
+
+        pbs = new PositionalBufferedStream(new FileInputStream(source));
+        pbs.skip(header.getHeaderEnd());
+
+        final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue();
+
+        while ( ! pbs.isDone() ) {
+            final VariantContext vc = codec.decode(pbs);
+            if ( vc != null )
+                vcs.add(vc);
+        }
+
+        return new Pair<VCFHeader, List<VariantContext>>(vcfHeader, vcs);
+    }
+}
\ No newline at end of file
diff --git a/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
new file mode 100644
index 000000000..47f766d9b
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -0,0 +1,450 @@
+package org.broadinstitute.sting.utils.variant;
+
+import com.google.java.contract.Requires;
+import org.apache.commons.lang.ArrayUtils;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.GenomeLocParser;
+import org.broadinstitute.sting.utils.MathUtils;
+import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.variant.variantcontext.*;
+
+import java.util.*;
+
+public class GATKVariantContextUtils {
+
+    public static final int DEFAULT_PLOIDY = 2;
+    public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
+    private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
+
+    /**
+     * create a genome location, given a variant context
+     * @param genomeLocParser parser
+     * @param vc the variant context
+     * @return the genomeLoc
+     */
+    public static final GenomeLoc getLocation(GenomeLocParser genomeLocParser,VariantContext vc) {
+        return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true);
+    }
+
+    /**
+     * Returns true iff VC is an non-complex indel where every allele represents an expansion or
+     * contraction of a series of identical bases in the reference.
+     *
+     * For example, suppose the ref bases are CTCTCTGA, which includes a 3x repeat of CTCTCT
+     *
+     * If VC = -/CT, then this function returns true because the CT insertion matches exactly the
+     * upcoming reference.
+     * If VC = -/CTA then this function returns false because the CTA isn't a perfect match
+     *
+     * Now consider deletions:
+     *
+     * If VC = CT/- then again the same logic applies and this returns true
+     * The case of CTA/- makes no sense because it doesn't actually match the reference bases.
+     *
+     * The logic of this function is pretty simple.  Take all of the non-null alleles in VC.  For
+     * each insertion allele of n bases, check if that allele matches the next n reference bases.
+     * For each deletion allele of n bases, check if this matches the reference bases at n - 2 n,
+     * as it must necessarily match the first n bases.  If this test returns true for all
+     * alleles you are a tandem repeat, otherwise you are not.
+     *
+     * @param vc
+     * @param refBasesStartingAtVCWithPad not this is assumed to include the PADDED reference
+     * @return
+     */
+    @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"})
+    public static boolean isTandemRepeat(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) {
+        final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1);
+        if ( ! vc.isIndel() ) // only indels are tandem repeats
+            return false;
+
+        final Allele ref = vc.getReference();
+
+        for ( final Allele allele : vc.getAlternateAlleles() ) {
+            if ( ! isRepeatAllele(ref, allele, refBasesStartingAtVCWithoutPad) )
+                return false;
+        }
+
+        // we've passed all of the tests, so we are a repeat
+        return true;
+    }
+
+    /**
+     *
+     * @param vc
+     * @param refBasesStartingAtVCWithPad
+     * @return
+     */
+    @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"})
+    public static Pair<List<Integer>,byte[]> getNumTandemRepeatUnits(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) {
+        final boolean VERBOSE = false;
+        final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1);
+        if ( ! vc.isIndel() ) // only indels are tandem repeats
+            return null;
+
+        final Allele refAllele = vc.getReference();
+        final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length());
+
+        byte[] repeatUnit = null;
+        final ArrayList<Integer> lengths = new ArrayList<Integer>();
+
+        for ( final Allele allele : vc.getAlternateAlleles() ) {
+            Pair<int[],byte[]> result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes());
+
+            final int[] repetitionCount = result.first;
+            // repetition count = 0 means allele is not a tandem expansion of context
+            if (repetitionCount[0] == 0 || repetitionCount[1] == 0)
+                return null;
+
+            if (lengths.size() == 0) {
+                lengths.add(repetitionCount[0]); // add ref allele length only once
+            }
+            lengths.add(repetitionCount[1]);  // add this alt allele's length
+
+            repeatUnit = result.second;
+            if (VERBOSE) {
+                System.out.println("RefContext:"+refBasesStartingAtVCWithoutPad);
+                System.out.println("Ref:"+refAllele.toString()+" Count:" + String.valueOf(repetitionCount[0]));
+                System.out.println("Allele:"+allele.toString()+" Count:" + String.valueOf(repetitionCount[1]));
+                System.out.println("RU:"+new String(repeatUnit));
+            }
+        }
+
+        return new Pair<List<Integer>, byte[]>(lengths,repeatUnit);
+    }
+
+    protected static Pair<int[],byte[]> getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) {
+         /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units.
+           Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)5.
+         */
+
+        byte[] longB;
+        // find first repeat unit based on either ref or alt, whichever is longer
+        if (altBases.length > refBases.length)
+            longB = altBases;
+        else
+            longB = refBases;
+
+        // see if non-null allele (either ref or alt, whichever is longer) can be decomposed into several identical tandem units
+        // for example, -*,CACA needs to first be decomposed into (CA)2
+        final int repeatUnitLength = findRepeatedSubstring(longB);
+        final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength);
+
+        final int[] repetitionCount = new int[2];
+//        repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext));
+//        repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext));
+        int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases);
+        repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext))-repetitionsInRef;
+        repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext))-repetitionsInRef;
+
+        return new Pair<int[], byte[]>(repetitionCount, repeatUnit);
+
+    }
+
+    /**
+     * Find out if a string can be represented as a tandem number of substrings.
+     * For example ACTACT is a 2-tandem of ACT,
+     * but ACTACA is not.
+     *
+     * @param bases                 String to be tested
+     * @return                      Length of repeat unit, if string can be represented as tandem of substring (if it can't
+     *                              be represented as one, it will be just the length of the input string)
+     */
+    public static int findRepeatedSubstring(byte[] bases) {
+
+        int repLength;
+        for (repLength=1; repLength <=bases.length; repLength++) {
+            final byte[] candidateRepeatUnit = Arrays.copyOf(bases,repLength);
+            boolean allBasesMatch = true;
+            for (int start = repLength; start < bases.length; start += repLength ) {
+                // check that remaining of string is exactly equal to repeat unit
+                final byte[] basePiece = Arrays.copyOfRange(bases,start,start+candidateRepeatUnit.length);
+                if (!Arrays.equals(candidateRepeatUnit, basePiece)) {
+                    allBasesMatch = false;
+                    break;
+                }
+            }
+            if (allBasesMatch)
+                return repLength;
+        }
+
+        return repLength;
+    }
+
+    /**
+     * Helper routine that finds number of repetitions a string consists of.
+     * For example, for string ATAT and repeat unit AT, number of repetitions = 2
+     * @param repeatUnit             Substring
+     * @param testString             String to test
+     * @return                       Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
+     */
+    public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
+        int numRepeats = 0;
+        for (int start = 0; start < testString.length; start += repeatUnit.length) {
+            int end = start + repeatUnit.length;
+            byte[] unit = Arrays.copyOfRange(testString,start, end);
+            if(Arrays.equals(unit,repeatUnit))
+                numRepeats++;
+            else
+                return numRepeats;
+        }
+        return numRepeats;
+    }
+
+    /**
+     * Helper function for isTandemRepeat that checks that allele matches somewhere on the reference
+     * @param ref
+     * @param alt
+     * @param refBasesStartingAtVCWithoutPad
+     * @return
+     */
+    protected static boolean isRepeatAllele(final Allele ref, final Allele alt, final String refBasesStartingAtVCWithoutPad) {
+        if ( ! Allele.oneIsPrefixOfOther(ref, alt) )
+            return false; // we require one allele be a prefix of another
+
+        if ( ref.length() > alt.length() ) { // we are a deletion
+            return basesAreRepeated(ref.getBaseString(), alt.getBaseString(), refBasesStartingAtVCWithoutPad, 2);
+        } else { // we are an insertion
+            return basesAreRepeated(alt.getBaseString(), ref.getBaseString(), refBasesStartingAtVCWithoutPad, 1);
+        }
+    }
+
+    protected static boolean basesAreRepeated(final String l, final String s, final String ref, final int minNumberOfMatches) {
+        final String potentialRepeat = l.substring(s.length()); // skip s bases
+
+        for ( int i = 0; i < minNumberOfMatches; i++) {
+            final int start = i * potentialRepeat.length();
+            final int end = (i+1) * potentialRepeat.length();
+            if ( ref.length() < end )
+                 return false; // we ran out of bases to test
+            final String refSub = ref.substring(start, end);
+            if ( ! refSub.equals(potentialRepeat) )
+                return false; // repeat didn't match, fail
+        }
+
+        return true; // we passed all tests, we matched
+    }
+
+    /**
+     * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
+     *
+     * @param vc            variant context with genotype likelihoods
+     * @return genotypes context
+     */
+    public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) {
+        return subsetDiploidAlleles(vc, vc.getAlleles(), true);
+    }
+
+    /**
+     * Split variant context into its biallelic components if there are more than 2 alleles
+     *
+     * For VC has A/B/C alleles, returns A/B and A/C contexts.
+     * Genotypes are all no-calls now (it's not possible to fix them easily)
+     * Alleles are right trimmed to satisfy VCF conventions
+     *
+     * If vc is biallelic or non-variant it is just returned
+     *
+     * Chromosome counts are updated (but they are by definition 0)
+     *
+     * @param vc a potentially multi-allelic variant context
+     * @return a list of bi-allelic (or monomorphic) variant context
+     */
+    public static List<VariantContext> splitVariantContextToBiallelics(final VariantContext vc) {
+        if ( ! vc.isVariant() || vc.isBiallelic() )
+            // non variant or biallelics already satisfy the contract
+            return Collections.singletonList(vc);
+        else {
+            final List<VariantContext> biallelics = new LinkedList<VariantContext>();
+
+            for ( final Allele alt : vc.getAlternateAlleles() ) {
+                VariantContextBuilder builder = new VariantContextBuilder(vc);
+                final List<Allele> alleles = Arrays.asList(vc.getReference(), alt);
+                builder.alleles(alleles);
+                builder.genotypes(subsetDiploidAlleles(vc, alleles, false));
+                VariantContextUtils.calculateChromosomeCounts(builder, true);
+                biallelics.add(reverseTrimAlleles(builder.make()));
+            }
+
+            return biallelics;
+        }
+    }
+
+    /**
+     * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
+     *
+     * @param vc                 variant context with genotype likelihoods
+     * @param allelesToUse       which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
+     * @param assignGenotypes    true if we should update the genotypes based on the (subsetted) PLs
+     * @return genotypes
+     */
+    public static GenotypesContext subsetDiploidAlleles(final VariantContext vc,
+                                                 final List<Allele> allelesToUse,
+                                                 final boolean assignGenotypes) {
+
+        // the genotypes with PLs
+        final GenotypesContext oldGTs = vc.getGenotypes();
+
+        // samples
+        final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
+
+        // the new genotypes to create
+        final GenotypesContext newGTs = GenotypesContext.create();
+
+        // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
+        final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
+        final int numNewAltAlleles = allelesToUse.size() - 1;
+
+        // which PLs should be carried forward?
+        ArrayList<Integer> likelihoodIndexesToUse = null;
+
+        // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
+        // then we can keep the PLs as is; otherwise, we determine which ones to keep
+        if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) {
+            likelihoodIndexesToUse = new ArrayList<Integer>(30);
+
+            final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles];
+            for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
+                if ( allelesToUse.contains(vc.getAlternateAllele(i)) )
+                    altAlleleIndexToUse[i] = true;
+            }
+
+            // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2
+            final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + numOriginalAltAlleles, DEFAULT_PLOIDY);
+            for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
+                final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
+                // consider this entry only if both of the alleles are good
+                if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) )
+                    likelihoodIndexesToUse.add(PLindex);
+            }
+        }
+
+        // create the new genotypes
+        for ( int k = 0; k < oldGTs.size(); k++ ) {
+            final Genotype g = oldGTs.get(sampleIndices.get(k));
+            if ( !g.hasLikelihoods() ) {
+                newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
+                continue;
+            }
+
+            // create the new likelihoods array from the alleles we are allowed to use
+            final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
+            double[] newLikelihoods;
+            if ( likelihoodIndexesToUse == null ) {
+                newLikelihoods = originalLikelihoods;
+            } else {
+                newLikelihoods = new double[likelihoodIndexesToUse.size()];
+                int newIndex = 0;
+                for ( int oldIndex : likelihoodIndexesToUse )
+                    newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
+
+                // might need to re-normalize
+                newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
+            }
+
+            // if there is no mass on the (new) likelihoods, then just no-call the sample
+            if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
+                newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
+            }
+            else {
+                final GenotypeBuilder gb = new GenotypeBuilder(g);
+
+                if ( numNewAltAlleles == 0 )
+                    gb.noPL();
+                else
+                    gb.PL(newLikelihoods);
+
+                // if we weren't asked to assign a genotype, then just no-call the sample
+                if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
+                    gb.alleles(NO_CALL_ALLELES);
+                }
+                else {
+                    // find the genotype with maximum likelihoods
+                    int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
+                    GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
+
+                    gb.alleles(Arrays.asList(allelesToUse.get(alleles.alleleIndex1), allelesToUse.get(alleles.alleleIndex2)));
+                    if ( numNewAltAlleles != 0 ) gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
+                }
+                newGTs.add(gb.make());
+            }
+        }
+
+        return newGTs;
+    }
+
+    public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) {
+
+        // see whether we need to trim common reference base from all alleles
+        final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, false);
+        if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 )
+            return inputVC;
+
+        final List<Allele> alleles = new ArrayList<Allele>();
+        final GenotypesContext genotypes = GenotypesContext.create();
+        final Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
+
+        for (final Allele a : inputVC.getAlleles()) {
+            if (a.isSymbolic()) {
+                alleles.add(a);
+                originalToTrimmedAlleleMap.put(a, a);
+            } else {
+                // get bases for current allele and create a new one with trimmed bases
+                final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent);
+                final Allele trimmedAllele = Allele.create(newBases, a.isReference());
+                alleles.add(trimmedAllele);
+                originalToTrimmedAlleleMap.put(a, trimmedAllele);
+            }
+        }
+
+        // now we can recreate new genotypes with trimmed alleles
+        for ( final Genotype genotype : inputVC.getGenotypes() ) {
+            final List<Allele> originalAlleles = genotype.getAlleles();
+            final List<Allele> trimmedAlleles = new ArrayList<Allele>();
+            for ( final Allele a : originalAlleles ) {
+                if ( a.isCalled() )
+                    trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
+                else
+                    trimmedAlleles.add(Allele.NO_CALL);
+            }
+            genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make());
+        }
+
+        return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() - 1).alleles(alleles).genotypes(genotypes).make();
+    }
+
+    public static int computeReverseClipping(final List<Allele> unclippedAlleles,
+                                             final byte[] ref,
+                                             final int forwardClipping,
+                                             final boolean allowFullClip) {
+        int clipping = 0;
+        boolean stillClipping = true;
+
+        while ( stillClipping ) {
+            for ( final Allele a : unclippedAlleles ) {
+                if ( a.isSymbolic() )
+                    continue;
+
+                // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong
+                // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine).
+                if ( a.length() - clipping == 0 )
+                    return clipping - (allowFullClip ? 0 : 1);
+
+                if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) {
+                    stillClipping = false;
+                }
+                else if ( ref.length == clipping ) {
+                    if ( allowFullClip )
+                        stillClipping = false;
+                    else
+                        return -1;
+                }
+                else if ( a.getBases()[a.length()-clipping-1] != ref[ref.length-clipping-1] ) {
+                    stillClipping = false;
+                }
+            }
+            if ( stillClipping )
+                clipping++;
+        }
+
+        return clipping;
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java
index c221b8fba..b8bc1be6b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Codec.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Codec.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
@@ -30,12 +30,11 @@ import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
 import org.broad.tribble.FeatureCodecHeader;
+import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.vcf.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.ByteArrayInputStream;
 import java.io.FileInputStream;
@@ -127,7 +126,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
             createLazyGenotypesDecoder(info, builder);
             return builder.fullyDecoded(true).make();
         } catch ( IOException e ) {
-            throw new UserException.CouldNotReadInputFile("Failed to read BCF file", e);
+            throw new TribbleException("Failed to read BCF file", e);
         }
     }
 
@@ -166,7 +165,7 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
             this.header = (VCFHeader)headerParser.readHeader(headerReader);
             bps.close();
         } catch ( IOException e ) {
-            throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 header");
+            throw new TribbleException("I/O error while reading BCF2 header");
         }
 
         // create the config offsets
@@ -271,8 +270,8 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
         final int nSamples = nFormatSamples & 0x00FFFFF;
 
         if ( header.getNGenotypeSamples() != nSamples )
-            error("GATK currently doesn't support reading BCF2 files with " +
-                    "different numbers of samples per record.  Saw " + header.getNGenotypeSamples() +
+            error("Reading BCF2 files with different numbers of samples per record " +
+                    "is not currently supported.  Saw " + header.getNGenotypeSamples() +
                     " samples in header but have a record with " + nSamples + " samples");
 
         decodeID(builder);
@@ -494,6 +493,6 @@ public final class BCF2Codec implements FeatureCodec<VariantContext> {
     }
 
     private void error(final String message) throws RuntimeException {
-        throw new UserException.MalformedBCF2(String.format("%s, at record %d with position %d:", message, recordNo, pos));
+        throw new TribbleException(String.format("%s, at record %d with position %d:", message, recordNo, pos));
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java
index 05ba2aa1f..ca5975ab0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Decoder.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Decoder.java
@@ -22,14 +22,13 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
 import org.broad.tribble.FeatureCodec;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broad.tribble.TribbleException;
 
 import java.io.ByteArrayInputStream;
 import java.io.IOException;
@@ -69,7 +68,7 @@ public final class BCF2Decoder {
      * @return
      */
     public void readNextBlock(final int blockSizeInBytes, final InputStream stream) {
-        if ( blockSizeInBytes < 0 ) throw new UserException.MalformedBCF2("Invalid block size " + blockSizeInBytes);
+        if ( blockSizeInBytes < 0 ) throw new TribbleException("Invalid block size " + blockSizeInBytes);
         setRecordBytes(readRecordBytes(blockSizeInBytes, stream));
     }
 
@@ -84,7 +83,7 @@ public final class BCF2Decoder {
             final int bytesRead = (int)stream.skip(blockSizeInBytes);
             validateReadBytes(bytesRead, 1, blockSizeInBytes);
         } catch ( IOException e ) {
-            throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e);
+            throw new TribbleException("I/O error while reading BCF2 file", e);
         }
         this.recordBytes = null;
         this.recordStream = null;
@@ -175,7 +174,7 @@ public final class BCF2Decoder {
                 case INT32: return value;
                 case FLOAT: return rawFloatToFloat(value);
                 case CHAR:  return value & 0xFF; // TODO -- I cannot imagine why we'd get here, as string needs to be special cased
-                default:    throw new ReviewedStingException("BCF2 codec doesn't know how to decode type " + type );
+                default:    throw new TribbleException("BCF2 codec doesn't know how to decode type " + type );
             }
         }
     }
@@ -205,7 +204,7 @@ public final class BCF2Decoder {
                 return BCF2Utils.isCollapsedString(s) ? BCF2Utils.explodeStringList(s) : s;
             }
         } catch ( IOException e ) {
-            throw new ReviewedStingException("readByte failure", e);
+            throw new TribbleException("readByte failure", e);
         }
     }
 
@@ -348,7 +347,7 @@ public final class BCF2Decoder {
 
             validateReadBytes(bytesRead, nReadAttempts, blockSizeInBytes);
         } catch ( IOException e ) {
-            throw new UserException.CouldNotReadInputFile("I/O error while reading BCF2 file", e);
+            throw new TribbleException("I/O error while reading BCF2 file", e);
         }
 
         return record;
@@ -365,7 +364,7 @@ public final class BCF2Decoder {
         assert expected >= 0;
 
         if ( actuallyRead < expected ) {
-            throw new UserException.MalformedBCF2(
+            throw new TribbleException(
                     String.format("Failed to read next complete record: expected %d bytes but read only %d after %d iterations",
                             expected, actuallyRead, nReadAttempts));
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java
index e4ae96262..9355d56de 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2GenotypeFieldDecoders.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2GenotypeFieldDecoders.java
@@ -22,15 +22,15 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.GenotypeBuilder;
 
 import java.io.IOException;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java
similarity index 89%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java
index 46b1fa6c1..c2d893b7f 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2LazyGenotypesDecoder.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2LazyGenotypesDecoder.java
@@ -22,13 +22,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broad.tribble.TribbleException;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.IOException;
 import java.util.*;
@@ -85,7 +84,7 @@ public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser
                 try {
                     fieldDecoder.decode(siteAlleles, field, decoder, typeDescriptor, numElements, builders);
                 } catch ( ClassCastException e ) {
-                    throw new UserException.MalformedBCF2("BUG: expected encoding of field " + field
+                    throw new TribbleException("BUG: expected encoding of field " + field
                             + " inconsistent with the value observed in the decoded value");
                 }
             }
@@ -96,7 +95,7 @@ public class BCF2LazyGenotypesDecoder implements LazyGenotypesContext.LazyParser
 
             return new LazyGenotypesContext.LazyData(genotypes, codec.getHeader().getSampleNamesInOrder(), codec.getHeader().getSampleNameToOffset());
         } catch ( IOException e ) {
-            throw new ReviewedStingException("Unexpected IOException parsing already read genotypes data block", e);
+            throw new TribbleException("Unexpected IOException parsing already read genotypes data block", e);
         }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Type.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Type.java
index 1162a5d1e..b24f2a582 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Type.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Type.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import com.google.java.contract.Requires;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Utils.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCF2Utils.java
index 2ac916db1..30d6b4ee4 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCF2Utils.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCF2Utils.java
@@ -22,12 +22,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broad.tribble.TribbleException;
+import org.broadinstitute.variant.vcf.*;
 
 import java.io.*;
 import java.util.*;
@@ -214,7 +214,7 @@ public final class BCF2Utils {
                 return potentialType;
         }
 
-        throw new ReviewedStingException("Integer cannot be encoded in allowable range of even INT32: " + value);
+        throw new TribbleException("Integer cannot be encoded in allowable range of even INT32: " + value);
     }
 
     @Ensures("result.isIntegerType()")
@@ -249,7 +249,7 @@ public final class BCF2Utils {
             case INT8: return t2;
             case INT16: return t2 == BCF2Type.INT32 ? t2 : t1;
             case INT32: return t1;
-            default: throw new ReviewedStingException("BUG: unexpected BCF2Type " + t1);
+            default: throw new TribbleException("BUG: unexpected BCF2Type " + t1);
         }
     }
 
@@ -262,7 +262,7 @@ public final class BCF2Utils {
                 case INT8: break;
                 case INT16: maxType = BCF2Type.INT16; break;
                 case INT32: return BCF2Type.INT32; // fast path for largest possible value
-                default: throw new ReviewedStingException("Unexpected integer type " + type1 );
+                default: throw new TribbleException("Unexpected integer type " + type1 );
             }
         }
         return maxType;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java b/public/java/src/org/broadinstitute/variant/bcf2/BCFVersion.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java
rename to public/java/src/org/broadinstitute/variant/bcf2/BCFVersion.java
index 742da7c0c..5e1915c22 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/bcf2/BCFVersion.java
+++ b/public/java/src/org/broadinstitute/variant/bcf2/BCFVersion.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 import java.io.IOException;
 import java.io.InputStream;
diff --git a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java b/public/java/src/org/broadinstitute/variant/utils/BaseUtils.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
rename to public/java/src/org/broadinstitute/variant/utils/BaseUtils.java
index 53a49d8b2..4786622b0 100644
--- a/public/java/src/org/broadinstitute/sting/utils/BaseUtils.java
+++ b/public/java/src/org/broadinstitute/variant/utils/BaseUtils.java
@@ -1,10 +1,9 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.variant.utils;
 
 import net.sf.samtools.util.StringUtil;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.Arrays;
+import java.util.Random;
 
 /**
  * BaseUtils contains some basic utilities for manipulating nucleotides.
@@ -47,6 +46,9 @@ public class BaseUtils {
     public static final int gIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'G');
     public static final int tIndex = BaseUtils.simpleBaseToBaseIndex((byte) 'T');
 
+    // Use a fixed random seed to allow for deterministic results when using random bases
+    private static final Random randomNumberGen = new Random(47382911L);
+
     /// In genetics, a transition is a mutation changing a purine to another purine nucleotide (A <-> G) or
     // a pyrimidine to another pyrimidine nucleotide (C <-> T).
     // Approximately two out of every three single nucleotide polymorphisms (SNPs) are transitions.
@@ -185,7 +187,7 @@ public class BaseUtils {
      */
     static public int simpleBaseToBaseIndex(final byte base) {
         if ( base < 0 || base >= 256 )
-            throw new UserException.BadInput("Non-standard bases were encountered in either the input reference or BAM file(s)");
+            throw new IllegalArgumentException("Non-standard bases were encountered in either the input reference or BAM file(s)");
         return baseIndexMap[base];
     }
 
@@ -425,7 +427,7 @@ public class BaseUtils {
         int randomBaseIndex = excludeBaseIndex;
 
         while (randomBaseIndex == excludeBaseIndex) {
-            randomBaseIndex = GenomeAnalysisEngine.getRandomGenerator().nextInt(4);
+            randomBaseIndex = randomNumberGen.nextInt(4);
         }
 
         return randomBaseIndex;
diff --git a/public/java/src/org/broadinstitute/variant/utils/Utils.java b/public/java/src/org/broadinstitute/variant/utils/Utils.java
new file mode 100644
index 000000000..1272429cb
--- /dev/null
+++ b/public/java/src/org/broadinstitute/variant/utils/Utils.java
@@ -0,0 +1,130 @@
+package org.broadinstitute.variant.utils;
+
+import java.util.Collection;
+import java.util.Iterator;
+
+public class Utils {
+
+    /**
+     * The smallest log10 value we'll emit from normalizeFromLog10 and other functions
+     * where the real-space value is 0.0.
+     */
+    public final static double LOG10_P_OF_ZERO = -1000000.0;
+
+    /**
+     * Returns a string of the form elt1.toString() [sep elt2.toString() ... sep elt.toString()] for a collection of
+     * elti objects (note there's no actual space between sep and the elti elements).  Returns
+     * "" if collection is empty.  If collection contains just elt, then returns elt.toString()
+     *
+     * @param separator the string to use to separate objects
+     * @param objects a collection of objects.  the element order is defined by the iterator over objects
+     * @param <T> the type of the objects
+     * @return a non-null string
+     */
+    public static <T> String join(final String separator, final Collection<T> objects) {
+        if (objects.isEmpty()) { // fast path for empty collection
+            return "";
+        } else {
+            final Iterator<T> iter = objects.iterator();
+            final T first = iter.next();
+
+            if ( ! iter.hasNext() ) // fast path for singleton collections
+                return first.toString();
+            else { // full path for 2+ collection that actually need a join
+                final StringBuilder ret = new StringBuilder(first.toString());
+                while(iter.hasNext()) {
+                    ret.append(separator);
+                    ret.append(iter.next().toString());
+                }
+                return ret.toString();
+            }
+        }
+    }
+
+
+    /**
+     * normalizes the log10-based array.  ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE).
+     *
+     * @param array the array to be normalized
+     * @return a newly allocated array corresponding the normalized values in array
+     */
+    public static double[] normalizeFromLog10(double[] array) {
+        return normalizeFromLog10(array, false);
+    }
+
+    /**
+     * normalizes the log10-based array.  ASSUMES THAT ALL ARRAY ENTRIES ARE <= 0 (<= 1 IN REAL-SPACE).
+     *
+     * @param array             the array to be normalized
+     * @param takeLog10OfOutput if true, the output will be transformed back into log10 units
+     * @return a newly allocated array corresponding the normalized values in array, maybe log10 transformed
+     */
+    public static double[] normalizeFromLog10(double[] array, boolean takeLog10OfOutput) {
+        return normalizeFromLog10(array, takeLog10OfOutput, false);
+    }
+
+    /**
+     * See #normalizeFromLog10 but with the additional option to use an approximation that keeps the calculation always in log-space
+     *
+     * @param array
+     * @param takeLog10OfOutput
+     * @param keepInLogSpace
+     *
+     * @return
+     */
+    public static double[] normalizeFromLog10(double[] array, boolean takeLog10OfOutput, boolean keepInLogSpace) {
+        // for precision purposes, we need to add (or really subtract, since they're
+        // all negative) the largest value; also, we need to convert to normal-space.
+        double maxValue = arrayMax(array);
+
+        // we may decide to just normalize in log space without converting to linear space
+        if (keepInLogSpace) {
+            for (int i = 0; i < array.length; i++) {
+                array[i] -= maxValue;
+            }
+            return array;
+        }
+
+        // default case: go to linear space
+        double[] normalized = new double[array.length];
+
+        for (int i = 0; i < array.length; i++)
+            normalized[i] = Math.pow(10, array[i] - maxValue);
+
+        // normalize
+        double sum = 0.0;
+        for (int i = 0; i < array.length; i++)
+            sum += normalized[i];
+        for (int i = 0; i < array.length; i++) {
+            double x = normalized[i] / sum;
+            if (takeLog10OfOutput) {
+                x = Math.log10(x);
+                if ( x < LOG10_P_OF_ZERO || Double.isInfinite(x) )
+                    x = array[i] - maxValue;
+            }
+
+            normalized[i] = x;
+        }
+
+        return normalized;
+    }
+
+    public static double arrayMax(final double[] array) {
+        return array[maxElementIndex(array, array.length)];
+    }
+
+    public static int maxElementIndex(final double[] array, final int endIndex) {
+        if (array == null || array.length == 0)
+            throw new IllegalArgumentException("Array cannot be null!");
+
+        int maxI = 0;
+        for (int i = 1; i < endIndex; i++) {
+            if (array[i] > array[maxI])
+                maxI = i;
+        }
+
+        return maxI;
+    }
+}
+
+
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java b/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/Allele.java
index 85c925204..b231019b8 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Allele.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/Allele.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 
 import java.util.Arrays;
 import java.util.Collection;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java b/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java
index 127f91677..3cc54384f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/CommonInfo.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/CommonInfo.java
@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java b/public/java/src/org/broadinstitute/variant/variantcontext/FastGenotype.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/FastGenotype.java
index 4a7df9da4..8d8a8bbfb 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/FastGenotype.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/FastGenotype.java
@@ -22,11 +22,10 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java b/public/java/src/org/broadinstitute/variant/variantcontext/Genotype.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/Genotype.java
index 67e80cf3c..4f83fa7be 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/Genotype.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/Genotype.java
@@ -1,12 +1,11 @@
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.util.*;
 
@@ -209,7 +208,7 @@ public abstract class Genotype implements Comparable<Genotype> {
         }
 
         if ( observedAllele == null )
-            throw new ReviewedStingException("BUG: there are no alleles present in this genotype but the alleles list is not null");
+            throw new IllegalStateException("BUG: there are no alleles present in this genotype but the alleles list is not null");
 
         return sawMultipleAlleles ? GenotypeType.HET : observedAllele.isReference() ? GenotypeType.HOM_REF : GenotypeType.HOM_VAR;
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeBuilder.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypeBuilder.java
index 8fd792d3b..b8af1a305 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeBuilder.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeBuilder.java
@@ -22,14 +22,14 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.util.*;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java
index 641eb5449..287105dde 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeLikelihoods.java
@@ -22,15 +22,13 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.utils.MathUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.variant.utils.Utils;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.util.Arrays;
 import java.util.EnumMap;
@@ -156,7 +154,7 @@ public class GenotypeLikelihoods {
     //Returns null in case of missing likelihoods
     public EnumMap<GenotypeType,Double> getAsMap(boolean normalizeFromLog10){
         //Make sure that the log10likelihoods are set
-        double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector();
+        double[] likelihoods = normalizeFromLog10 ? Utils.normalizeFromLog10(getAsVector()) : getAsVector();
         if(likelihoods == null)
             return null;
         EnumMap<GenotypeType,Double> likelihoodsMap = new EnumMap<GenotypeType, Double>(GenotypeType.class);
@@ -216,7 +214,7 @@ public class GenotypeLikelihoods {
         if (qual < 0) {
             // QUAL can be negative if the chosen genotype is not the most likely one individually.
             // In this case, we compute the actual genotype probability and QUAL is the likelihood of it not being the chosen one
-            double[] normalized = MathUtils.normalizeFromLog10(likelihoods);
+            double[] normalized = Utils.normalizeFromLog10(likelihoods);
             double chosenGenotype = normalized[iOfChoosenGenotype];
             return Math.log10(1.0 - chosenGenotype);
         } else {
@@ -234,7 +232,7 @@ public class GenotypeLikelihoods {
                     likelihoodsAsVector[i] = Integer.parseInt(strings[i]) / -10.0;
                 }
             } catch (NumberFormatException e) {
-                throw new UserException.MalformedVCF("The GL/PL tag contains non-integer values: " + likelihoodsAsString_PLs);
+                throw new TribbleException("The GL/PL tag contains non-integer values: " + likelihoodsAsString_PLs);
             }
             return likelihoodsAsVector;
         } else
@@ -335,7 +333,7 @@ public class GenotypeLikelihoods {
         // a bit of sanity checking
         for ( int i = 0; i < cache.length; i++ ) {
             if ( cache[i] == null )
-                throw new ReviewedStingException("BUG: cache entry " + i + " is unexpected null");
+                throw new IllegalStateException("BUG: cache entry " + i + " is unexpected null");
         }
 
         return cache;
@@ -422,7 +420,7 @@ public class GenotypeLikelihoods {
     public static GenotypeLikelihoodsAllelePair getAllelePair(final int PLindex) {
         // make sure that we've cached enough data
         if ( PLindex >= PLIndexToAlleleIndex.length )
-            throw new ReviewedStingException("GATK limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
+            throw new IllegalStateException("Internal limitation: cannot genotype more than " + MAX_ALT_ALLELES_THAT_CAN_BE_GENOTYPED + " alleles");
 
         return PLIndexToAlleleIndex[PLindex];
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeType.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeType.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeType.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypeType.java
index 1e3f43065..53798015e 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeType.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypeType.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 /**
  * Summary types for Genotype objects
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypesContext.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/GenotypesContext.java
index f306bac4d..d7239b2f3 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypesContext.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/GenotypesContext.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/LazyGenotypesContext.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/LazyGenotypesContext.java
index 1f73ecabd..8ecca17ca 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/LazyGenotypesContext.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/LazyGenotypesContext.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java
index 12f9cb20c..f0588f840 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContext.java
@@ -1,12 +1,10 @@
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import org.apache.log4j.Logger;
 import org.broad.tribble.Feature;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.variant.vcf.*;
 
 import java.util.*;
 
@@ -1156,7 +1154,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
                 if ( WARN_ABOUT_BAD_END )
                     logger.warn(message);
                 else
-                    throw new ReviewedStingException(message);
+                    throw new TribbleException(message);
             }
         } else {
             final long length = (stop - start) + 1;
@@ -1387,7 +1385,7 @@ public class VariantContext implements Feature { // to enable tribble integratio
                 final int obsSize = decoded instanceof List ? ((List) decoded).size() : 1;
                 final int expSize = format.getCount(this);
                 if ( obsSize != expSize ) {
-                    throw new UserException.MalformedVCFHeader("Discordant field size detected for field " +
+                    throw new TribbleException.InvalidHeader("Discordant field size detected for field " +
                             field + " at " + getChr() + ":" + getStart() + ".  Field had " + obsSize + " values " +
                             "but the header says this should have " + expSize + " values based on header record " +
                             format);
@@ -1437,17 +1435,17 @@ public class VariantContext implements Feature { // to enable tribble integratio
                     case Flag:
                         final boolean b = Boolean.valueOf(string) || string.equals("1");
                         if ( b == false )
-                            throw new UserException.MalformedVCF("VariantContext FLAG fields " + field + " cannot contain false values"
+                            throw new TribbleException("VariantContext FLAG fields " + field + " cannot contain false values"
                              + " as seen at " + getChr() + ":" + getStart());
                         return b;
                     case String:    return string;
                     case Integer:   return Integer.valueOf(string);
                     case Float:     return Double.valueOf(string);
-                    default: throw new ReviewedStingException("Unexpected type for field" + field);
+                    default: throw new TribbleException("Unexpected type for field" + field);
                 }
             }
         } catch (NumberFormatException e) {
-            throw new UserException.MalformedVCF("Could not decode field " + field + " with value " + string + " of declared type " + format.getType());
+            throw new TribbleException("Could not decode field " + field + " with value " + string + " of declared type " + format.getType());
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextBuilder.java
similarity index 93%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantContextBuilder.java
index 40ac089ef..bd12b8be5 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextBuilder.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextBuilder.java
@@ -22,12 +22,10 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import com.google.java.contract.*;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.util.*;
 
@@ -105,7 +103,7 @@ public class VariantContextBuilder {
      * @param parent  Cannot be null
      */
     public VariantContextBuilder(VariantContext parent) {
-        if ( parent == null ) throw new ReviewedStingException("BUG: VariantContextBuilder parent argument cannot be null in VariantContextBuilder");
+        if ( parent == null ) throw new IllegalArgumentException("BUG: VariantContextBuilder parent argument cannot be null in VariantContextBuilder");
         this.alleles = parent.alleles;
         this.attributes = parent.getAttributes();
         this.attributesCanBeModified = false;
@@ -121,7 +119,7 @@ public class VariantContextBuilder {
     }
 
     public VariantContextBuilder(VariantContextBuilder parent) {
-        if ( parent == null ) throw new ReviewedStingException("BUG: VariantContext parent argument cannot be null in VariantContextBuilder");
+        if ( parent == null ) throw new IllegalArgumentException("BUG: VariantContext parent argument cannot be null in VariantContextBuilder");
         this.alleles = parent.alleles;
         this.attributesCanBeModified = false;
         this.contig = parent.contig;
@@ -384,20 +382,6 @@ public class VariantContextBuilder {
         return this;
     }
 
-    /**
-     * Tells us that the resulting VariantContext should have the specified location
-     * @param loc
-     * @return
-     */
-    @Requires({"loc.getContig() != null", "loc.getStart() >= 0", "loc.getStop() >= 0"})
-    public VariantContextBuilder loc(final GenomeLoc loc) {
-        this.contig = loc.getContig();
-        this.start = loc.getStart();
-        this.stop = loc.getStop();
-        toValidate.add(VariantContext.Validation.ALLELES);
-        return this;
-    }
-
     /**
      * Tells us that the resulting VariantContext should have the specified contig chr
      * @param contig
@@ -442,8 +426,6 @@ public class VariantContextBuilder {
     /**
      * Compute the end position for this VariantContext from the alleles themselves
      *
-     * @see VariantContextUtils.computeEndFromAlleles()
-     *
      * assigns this builder the stop position computed.
      *
      * @param alleles the list of alleles to consider.  The reference allele must be the first one
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
similarity index 66%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
index 8b360eb5e..5d9a6d476 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantContextUtils.java
@@ -21,21 +21,18 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.commons.jexl2.Expression;
 import org.apache.commons.jexl2.JexlEngine;
-import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
+import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
-import org.broadinstitute.sting.commandline.Hidden;
-import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.variant.utils.BaseUtils;
+import org.broadinstitute.variant.utils.Utils;
+import org.broadinstitute.variant.vcf.*;
 
 import java.io.Serializable;
 import java.util.*;
@@ -50,7 +47,6 @@ public class VariantContextUtils {
     private static Set<String> MISSING_KEYS_WARNED_ABOUT = new HashSet<String>();
 
     final public static JexlEngine engine = new JexlEngine();
-    public static final int DEFAULT_PLOIDY = 2;
     private final static boolean ASSUME_MISSING_FIELDS_ARE_STRINGS = false;
 
     static {
@@ -173,7 +169,7 @@ public class VariantContextUtils {
                 return new VCFInfoHeaderLine(field, VCFHeaderLineCount.UNBOUNDED, VCFHeaderLineType.String, "Auto-generated string header for " + field);
             }
             else
-                throw new UserException.MalformedVCF("Fully decoding VariantContext requires header line for all fields, but none was found for " + field);
+                throw new TribbleException("Fully decoding VariantContext requires header line for all fields, but none was found for " + field);
         }
         return metaData;
     }
@@ -208,10 +204,10 @@ public class VariantContextUtils {
      */
     public static List<JexlVCMatchExp> initializeMatchExps(String[] names, String[] exps) {
         if ( names == null || exps == null )
-            throw new ReviewedStingException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) );
+            throw new IllegalArgumentException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) );
 
         if ( names.length != exps.length )
-            throw new UserException("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps));
+            throw new IllegalArgumentException("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps));
 
         Map<String, String> map = new HashMap<String, String>();
         for ( int i = 0; i < names.length; i++ ) { map.put(names[i], exps[i]); }
@@ -247,7 +243,7 @@ public class VariantContextUtils {
                 Expression exp = engine.createExpression(expStr);
                 exps.add(new JexlVCMatchExp(name, exp));
             } catch (Exception e) {
-                throw new UserException.BadArgumentValue(name, "Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ;
+                throw new IllegalArgumentException("Argument " + name + "has a bad value. Invalid expression used (" + expStr + "). Please see the JEXL docs for correct syntax.") ;
             }
         }
 
@@ -409,7 +405,6 @@ public class VariantContextUtils {
         KEEP_UNCONDITIONAL
     }
 
-    @Hidden
     public enum MultipleAllelesMergeType {
         /**
          * Combine only alleles of the same type (SNP, indel, etc.) into a single VCF record.
@@ -426,7 +421,6 @@ public class VariantContextUtils {
      * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
      * the sample name
      *
-     * @param genomeLocParser           loc parser
      * @param unsortedVCs               collection of unsorted VCs
      * @param priorityListOfVCs         priority list detailing the order in which we should grab the VCs
      * @param filteredRecordMergeType   merge type for filtered records
@@ -438,8 +432,7 @@ public class VariantContextUtils {
      * @param mergeInfoWithMaxAC        should we merge in info from the VC with maximum allele count?
      * @return new VariantContext       representing the merge of unsortedVCs
      */
-    public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser,
-                                             final Collection<VariantContext> unsortedVCs,
+    public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs,
                                              final List<String> priorityListOfVCs,
                                              final FilteredRecordMergeType filteredRecordMergeType,
                                              final GenotypeMergeType genotypeMergeOptions,
@@ -449,7 +442,7 @@ public class VariantContextUtils {
                                              final boolean filteredAreUncalled,
                                              final boolean mergeInfoWithMaxAC ) {
         int originalNumOfVCs = priorityListOfVCs == null ? 0 : priorityListOfVCs.size();
-        return simpleMerge(genomeLocParser,unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC);
+        return simpleMerge(unsortedVCs,priorityListOfVCs,originalNumOfVCs,filteredRecordMergeType,genotypeMergeOptions,annotateOrigin,printMessages,setKey,filteredAreUncalled,mergeInfoWithMaxAC);
     }
 
     /**
@@ -457,7 +450,6 @@ public class VariantContextUtils {
      * If uniquifySamples is true, the priority order is ignored and names are created by concatenating the VC name with
      * the sample name
      *
-     * @param genomeLocParser           loc parser
      * @param unsortedVCs               collection of unsorted VCs
      * @param priorityListOfVCs         priority list detailing the order in which we should grab the VCs
      * @param filteredRecordMergeType   merge type for filtered records
@@ -469,8 +461,7 @@ public class VariantContextUtils {
      * @param mergeInfoWithMaxAC        should we merge in info from the VC with maximum allele count?
      * @return new VariantContext       representing the merge of unsortedVCs
      */
-    public static VariantContext simpleMerge(final GenomeLocParser genomeLocParser,
-                                             final Collection<VariantContext> unsortedVCs,
+    public static VariantContext simpleMerge(final Collection<VariantContext> unsortedVCs,
                                              final List<String> priorityListOfVCs,
                                              final int originalNumOfVCs,
                                              final FilteredRecordMergeType filteredRecordMergeType,
@@ -517,7 +508,7 @@ public class VariantContextUtils {
         final Set<String> variantSources = new HashSet<String>(); // contains the set of sources we found in our set of VCs that are variant
         final Set<String> rsIDs = new LinkedHashSet<String>(1); // most of the time there's one id
 
-        GenomeLoc loc = getLocation(genomeLocParser,first);
+        VariantContext longestVC = first;
         int depth = 0;
         int maxAC = -1;
         final Map<String, Object> attributesWithMaxAC = new LinkedHashMap<String, Object>();
@@ -533,11 +524,11 @@ public class VariantContextUtils {
         // cycle through and add info from the other VCs, making sure the loc/reference matches
 
         for ( final VariantContext vc : VCs ) {
-            if ( loc.getStart() != vc.getStart() )
-                throw new ReviewedStingException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
+            if ( longestVC.getStart() != vc.getStart() )
+                throw new IllegalStateException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
 
-            if ( getLocation(genomeLocParser,vc).size() > loc.size() )
-                loc = getLocation(genomeLocParser,vc); // get the longest location
+            if ( getSize(vc) > getSize(longestVC) )
+                longestVC = vc; // get the longest location
 
             nFiltered += vc.isFiltered() ? 1 : 0;
             if ( vc.isVariant() ) variantSources.add(vc.getSource());
@@ -612,8 +603,8 @@ public class VariantContextUtils {
                 continue;
             if ( hasPLIncompatibleAlleles(alleles, vc.alleles)) {
                 if ( ! genotypes.isEmpty() )
-                    logger.debug(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
-                            genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
+                    logger.debug(String.format("Stripping PLs at %s:%d-%d due to incompatible alleles merged=%s vs. single=%s",
+                            vc.getChr(), vc.getStart(), vc.getEnd(), alleles, vc.alleles));
                 genotypes = stripPLsAndAD(genotypes);
                 // this will remove stale AC,AF attributed from vc
                 calculateChromosomeCounts(vc, attributes, true);
@@ -661,7 +652,7 @@ public class VariantContextUtils {
         final String ID = rsIDs.isEmpty() ? VCFConstants.EMPTY_ID_FIELD : Utils.join(",", rsIDs);
 
         final VariantContextBuilder builder = new VariantContextBuilder().source(name).id(ID);
-        builder.loc(loc.getContig(), loc.getStart(), loc.getStop());
+        builder.loc(longestVC.getChr(), longestVC.getStart(), longestVC.getEnd());
         builder.alleles(alleles);
         builder.genotypes(genotypes);
         builder.log10PError(log10PError);
@@ -788,7 +779,7 @@ public class VariantContextUtils {
             for ( String name : vc.getSampleNames() ) {
                 //System.out.printf("Checking %s %b%n", name, names.contains(name));
                 if ( names.contains(name) )
-                    throw new UserException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name);
+                    throw new IllegalStateException("REQUIRE_UNIQUE sample names is true but duplicate names were discovered " + name);
             }
 
             names.addAll(vc.getSampleNames());
@@ -804,7 +795,7 @@ public class VariantContextUtils {
             if ( ref == null || ref.length() < myRef.length() )
                 ref = myRef;
             else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
-                throw new UserException.BadInput(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef));
+                throw new TribbleException(String.format("The provided variant file(s) have inconsistent references for the same position(s) at %s:%d, %s vs. %s", vc.getChr(), vc.getStart(), ref, myRef));
         }
 
         return ref;
@@ -826,7 +817,7 @@ public class VariantContextUtils {
             //
 
             Allele myRef = vc.getReference();
-            if ( refAllele.length() <= myRef.length() ) throw new ReviewedStingException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele);
+            if ( refAllele.length() <= myRef.length() ) throw new IllegalStateException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele);
             byte[] extraBases = Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length());
 
 //            System.out.printf("Remapping allele at %s%n", vc);
@@ -863,7 +854,7 @@ public class VariantContextUtils {
 
         private int getIndex(VariantContext vc) {
             int i = priorityListOfVCs.indexOf(vc.getSource());
-            if ( i == -1 ) throw new UserException.BadArgumentValue(Utils.join(",", priorityListOfVCs), "Priority list " + priorityListOfVCs + " doesn't contain variant context " + vc.getSource());
+            if ( i == -1 ) throw new IllegalArgumentException("Priority list " + priorityListOfVCs + " doesn't contain variant context " + vc.getSource());
             return i;
         }
 
@@ -985,14 +976,8 @@ public class VariantContextUtils {
         return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
     }
 
-    /**
-     * create a genome location, given a variant context
-     * @param genomeLocParser parser
-     * @param vc the variant context
-     * @return the genomeLoc
-     */
-    public static final GenomeLoc getLocation(GenomeLocParser genomeLocParser,VariantContext vc) {
-        return genomeLocParser.createGenomeLoc(vc.getChr(), vc.getStart(), vc.getEnd(), true);
+    public static int getSize( VariantContext vc ) {
+        return vc.getEnd() - vc.getStart() + 1;
     }
 
     public static final Set<String> genotypeNames(final Collection<Genotype> genotypes) {
@@ -1002,354 +987,6 @@ public class VariantContextUtils {
         return names;
     }
 
-    /**
-     * Assign genotypes (GTs) to the samples in the Variant Context greedily based on the PLs
-     *
-     * @param vc            variant context with genotype likelihoods
-     * @return genotypes context
-     */
-    public static GenotypesContext assignDiploidGenotypes(final VariantContext vc) {
-        return subsetDiploidAlleles(vc, vc.getAlleles(), true);
-    }
-
-    private static final List<Allele> NO_CALL_ALLELES = Arrays.asList(Allele.NO_CALL, Allele.NO_CALL);
-    public static final double SUM_GL_THRESH_NOCALL = -0.1; // if sum(gl) is bigger than this threshold, we treat GL's as non-informative and will force a no-call.
-
-    /**
-     * Split variant context into its biallelic components if there are more than 2 alleles
-     *
-     * For VC has A/B/C alleles, returns A/B and A/C contexts.
-     * Genotypes are all no-calls now (it's not possible to fix them easily)
-     * Alleles are right trimmed to satisfy VCF conventions
-     *
-     * If vc is biallelic or non-variant it is just returned
-     *
-     * Chromosome counts are updated (but they are by definition 0)
-     *
-     * @param vc a potentially multi-allelic variant context
-     * @return a list of bi-allelic (or monomorphic) variant context
-     */
-    public static List<VariantContext> splitVariantContextToBiallelics(final VariantContext vc) {
-        if ( ! vc.isVariant() || vc.isBiallelic() )
-            // non variant or biallelics already satisfy the contract
-            return Collections.singletonList(vc);
-        else {
-            final List<VariantContext> biallelics = new LinkedList<VariantContext>();
-
-            for ( final Allele alt : vc.getAlternateAlleles() ) {
-                VariantContextBuilder builder = new VariantContextBuilder(vc);
-                final List<Allele> alleles = Arrays.asList(vc.getReference(), alt);
-                builder.alleles(alleles);
-                builder.genotypes(VariantContextUtils.subsetDiploidAlleles(vc, alleles, false));
-                calculateChromosomeCounts(builder, true);
-                biallelics.add(reverseTrimAlleles(builder.make()));
-            }
-
-            return biallelics;
-        }
-    }
-
-    /**
-     * subset the Variant Context to the specific set of alleles passed in (pruning the PLs appropriately)
-     *
-     * @param vc                 variant context with genotype likelihoods
-     * @param allelesToUse       which alleles from the vc are okay to use; *** must be in the same relative order as those in the original VC ***
-     * @param assignGenotypes    true if we should update the genotypes based on the (subsetted) PLs
-     * @return genotypes
-     */
-    public static GenotypesContext subsetDiploidAlleles(final VariantContext vc,
-                                                 final List<Allele> allelesToUse,
-                                                 final boolean assignGenotypes) {
-
-        // the genotypes with PLs
-        final GenotypesContext oldGTs = vc.getGenotypes();
-
-        // samples
-        final List<String> sampleIndices = oldGTs.getSampleNamesOrderedByName();
-
-        // the new genotypes to create
-        final GenotypesContext newGTs = GenotypesContext.create();
-
-        // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
-        final int numOriginalAltAlleles = vc.getAlternateAlleles().size();
-        final int numNewAltAlleles = allelesToUse.size() - 1;
-
-        // which PLs should be carried forward?
-        ArrayList<Integer> likelihoodIndexesToUse = null;
-
-        // an optimization: if we are supposed to use all (or none in the case of a ref call) of the alleles,
-        // then we can keep the PLs as is; otherwise, we determine which ones to keep
-        if ( numNewAltAlleles != numOriginalAltAlleles && numNewAltAlleles > 0 ) {
-            likelihoodIndexesToUse = new ArrayList<Integer>(30);
-
-            final boolean[] altAlleleIndexToUse = new boolean[numOriginalAltAlleles];
-            for ( int i = 0; i < numOriginalAltAlleles; i++ ) {
-                if ( allelesToUse.contains(vc.getAlternateAllele(i)) )
-                    altAlleleIndexToUse[i] = true;
-            }
-
-            // numLikelihoods takes total # of alleles. Use default # of chromosomes (ploidy) = 2
-            final int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + numOriginalAltAlleles, DEFAULT_PLOIDY);
-            for ( int PLindex = 0; PLindex < numLikelihoods; PLindex++ ) {
-                final GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
-                // consider this entry only if both of the alleles are good
-                if ( (alleles.alleleIndex1 == 0 || altAlleleIndexToUse[alleles.alleleIndex1 - 1]) && (alleles.alleleIndex2 == 0 || altAlleleIndexToUse[alleles.alleleIndex2 - 1]) )
-                    likelihoodIndexesToUse.add(PLindex);
-            }
-        }
-
-        // create the new genotypes
-        for ( int k = 0; k < oldGTs.size(); k++ ) {
-            final Genotype g = oldGTs.get(sampleIndices.get(k));
-            if ( !g.hasLikelihoods() ) {
-                newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
-                continue;
-            }
-
-            // create the new likelihoods array from the alleles we are allowed to use
-            final double[] originalLikelihoods = g.getLikelihoods().getAsVector();
-            double[] newLikelihoods;
-            if ( likelihoodIndexesToUse == null ) {
-                newLikelihoods = originalLikelihoods;
-            } else {
-                newLikelihoods = new double[likelihoodIndexesToUse.size()];
-                int newIndex = 0;
-                for ( int oldIndex : likelihoodIndexesToUse )
-                    newLikelihoods[newIndex++] = originalLikelihoods[oldIndex];
-
-                // might need to re-normalize
-                newLikelihoods = MathUtils.normalizeFromLog10(newLikelihoods, false, true);
-            }
-
-            // if there is no mass on the (new) likelihoods, then just no-call the sample
-            if ( MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
-                newGTs.add(GenotypeBuilder.create(g.getSampleName(), NO_CALL_ALLELES));
-            }
-            else {
-                final GenotypeBuilder gb = new GenotypeBuilder(g);
-
-                if ( numNewAltAlleles == 0 )
-                    gb.noPL();
-                else
-                    gb.PL(newLikelihoods);
-
-                // if we weren't asked to assign a genotype, then just no-call the sample
-                if ( !assignGenotypes || MathUtils.sum(newLikelihoods) > SUM_GL_THRESH_NOCALL ) {
-                    gb.alleles(NO_CALL_ALLELES);
-                }
-                else {
-                    // find the genotype with maximum likelihoods
-                    int PLindex = numNewAltAlleles == 0 ? 0 : MathUtils.maxElementIndex(newLikelihoods);
-                    GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(PLindex);
-
-                    gb.alleles(Arrays.asList(allelesToUse.get(alleles.alleleIndex1), allelesToUse.get(alleles.alleleIndex2)));
-                    if ( numNewAltAlleles != 0 ) gb.log10PError(GenotypeLikelihoods.getGQLog10FromLikelihoods(PLindex, newLikelihoods));
-                }
-                newGTs.add(gb.make());
-            }
-        }
-
-        return newGTs;
-    }
-
-    /**
-     * Returns true iff VC is an non-complex indel where every allele represents an expansion or 
-     * contraction of a series of identical bases in the reference.
-     * 
-     * For example, suppose the ref bases are CTCTCTGA, which includes a 3x repeat of CTCTCT
-     * 
-     * If VC = -/CT, then this function returns true because the CT insertion matches exactly the
-     * upcoming reference.  
-     * If VC = -/CTA then this function returns false because the CTA isn't a perfect match
-     * 
-     * Now consider deletions:
-     * 
-     * If VC = CT/- then again the same logic applies and this returns true
-     * The case of CTA/- makes no sense because it doesn't actually match the reference bases.  
-     * 
-     * The logic of this function is pretty simple.  Take all of the non-null alleles in VC.  For
-     * each insertion allele of n bases, check if that allele matches the next n reference bases.
-     * For each deletion allele of n bases, check if this matches the reference bases at n - 2 n,
-     * as it must necessarily match the first n bases.  If this test returns true for all 
-     * alleles you are a tandem repeat, otherwise you are not.
-     * 
-     * @param vc
-     * @param refBasesStartingAtVCWithPad not this is assumed to include the PADDED reference
-     * @return
-     */
-    @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"})
-    public static boolean isTandemRepeat(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) {
-        final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1);
-        if ( ! vc.isIndel() ) // only indels are tandem repeats
-            return false;
-        
-        final Allele ref = vc.getReference();
-
-        for ( final Allele allele : vc.getAlternateAlleles() ) {
-            if ( ! isRepeatAllele(ref, allele, refBasesStartingAtVCWithoutPad) )
-                return false;
-        }
-
-        // we've passed all of the tests, so we are a repeat
-        return true;
-    }
-
-    /**
-     *
-     * @param vc
-     * @param refBasesStartingAtVCWithPad
-     * @return
-     */
-    @Requires({"vc != null", "refBasesStartingAtVCWithPad != null && refBasesStartingAtVCWithPad.length > 0"})
-    public static Pair<List<Integer>,byte[]> getNumTandemRepeatUnits(final VariantContext vc, final byte[] refBasesStartingAtVCWithPad) {
-        final boolean VERBOSE = false;
-        final String refBasesStartingAtVCWithoutPad = new String(refBasesStartingAtVCWithPad).substring(1);
-        if ( ! vc.isIndel() ) // only indels are tandem repeats
-            return null;
-
-        final Allele refAllele = vc.getReference();
-        final byte[] refAlleleBases = Arrays.copyOfRange(refAllele.getBases(), 1, refAllele.length());
-
-        byte[] repeatUnit = null;
-        final ArrayList<Integer> lengths = new ArrayList<Integer>();
-
-        for ( final Allele allele : vc.getAlternateAlleles() ) {
-            Pair<int[],byte[]> result = getNumTandemRepeatUnits(refAlleleBases, Arrays.copyOfRange(allele.getBases(), 1, allele.length()), refBasesStartingAtVCWithoutPad.getBytes());
-
-            final int[] repetitionCount = result.first;
-            // repetition count = 0 means allele is not a tandem expansion of context
-            if (repetitionCount[0] == 0 || repetitionCount[1] == 0)
-                return null;
-
-            if (lengths.size() == 0) {
-                lengths.add(repetitionCount[0]); // add ref allele length only once
-            }
-            lengths.add(repetitionCount[1]);  // add this alt allele's length
-
-            repeatUnit = result.second;
-            if (VERBOSE) {
-                System.out.println("RefContext:"+refBasesStartingAtVCWithoutPad);
-                System.out.println("Ref:"+refAllele.toString()+" Count:" + String.valueOf(repetitionCount[0]));
-                System.out.println("Allele:"+allele.toString()+" Count:" + String.valueOf(repetitionCount[1]));
-                System.out.println("RU:"+new String(repeatUnit));
-            }
-        }
-
-        return new Pair<List<Integer>, byte[]>(lengths,repeatUnit);
-    }
-    
-    protected static Pair<int[],byte[]> getNumTandemRepeatUnits(final byte[] refBases, final byte[] altBases, final byte[] remainingRefContext) {
-         /* we can't exactly apply same logic as in basesAreRepeated() to compute tandem unit and number of repeated units.
-           Consider case where ref =ATATAT and we have an insertion of ATAT. Natural description is (AT)3 -> (AT)5.
-         */
-
-        byte[] longB;
-        // find first repeat unit based on either ref or alt, whichever is longer
-        if (altBases.length > refBases.length)
-            longB = altBases;
-        else
-            longB = refBases;
-
-        // see if non-null allele (either ref or alt, whichever is longer) can be decomposed into several identical tandem units
-        // for example, -*,CACA needs to first be decomposed into (CA)2 
-        final int repeatUnitLength = findRepeatedSubstring(longB);
-        final byte[] repeatUnit = Arrays.copyOf(longB, repeatUnitLength);
-
-        final int[] repetitionCount = new int[2];
-//        repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext));
-//        repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext));
-        int repetitionsInRef = findNumberofRepetitions(repeatUnit,refBases);
-        repetitionCount[0] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(refBases, remainingRefContext))-repetitionsInRef;
-        repetitionCount[1] = findNumberofRepetitions(repeatUnit, ArrayUtils.addAll(altBases, remainingRefContext))-repetitionsInRef;
-
-        return new Pair<int[], byte[]>(repetitionCount, repeatUnit);
-
-    }
-
-    /**
-     * Find out if a string can be represented as a tandem number of substrings.
-     * For example ACTACT is a 2-tandem of ACT,
-     * but ACTACA is not.
-     * 
-     * @param bases                 String to be tested
-     * @return                      Length of repeat unit, if string can be represented as tandem of substring (if it can't
-     *                              be represented as one, it will be just the length of the input string)
-     */
-    protected static int findRepeatedSubstring(byte[] bases) {
-        
-        int repLength;
-        for (repLength=1; repLength <=bases.length; repLength++) {
-            final byte[] candidateRepeatUnit = Arrays.copyOf(bases,repLength);
-            boolean allBasesMatch = true;
-            for (int start = repLength; start < bases.length; start += repLength ) {
-                // check that remaining of string is exactly equal to repeat unit
-                final byte[] basePiece = Arrays.copyOfRange(bases,start,start+candidateRepeatUnit.length);
-                if (!Arrays.equals(candidateRepeatUnit, basePiece)) {
-                    allBasesMatch = false;
-                    break;
-                }
-            }
-            if (allBasesMatch)
-                return repLength;
-        }
-        
-        return repLength;
-    }
-    
-    /**
-     * Helper routine that finds number of repetitions a string consists of.
-     * For example, for string ATAT and repeat unit AT, number of repetitions = 2
-     * @param repeatUnit             Substring
-     * @param testString             String to test
-     * @return                       Number of repetitions (0 if testString is not a concatenation of n repeatUnit's
-     */
-    public static int findNumberofRepetitions(byte[] repeatUnit, byte[] testString) {
-        int numRepeats = 0;
-        for (int start = 0; start < testString.length; start += repeatUnit.length) {
-            int end = start + repeatUnit.length;
-            byte[] unit = Arrays.copyOfRange(testString,start, end);
-            if(Arrays.equals(unit,repeatUnit))
-                numRepeats++;
-            else
-                return numRepeats;
-        }
-        return numRepeats;
-    }
-    
-    /**
-     * Helper function for isTandemRepeat that checks that allele matches somewhere on the reference
-     * @param ref
-     * @param alt
-     * @param refBasesStartingAtVCWithoutPad
-     * @return
-     */
-    protected static boolean isRepeatAllele(final Allele ref, final Allele alt, final String refBasesStartingAtVCWithoutPad) {
-        if ( ! Allele.oneIsPrefixOfOther(ref, alt) )
-            return false; // we require one allele be a prefix of another
-        
-        if ( ref.length() > alt.length() ) { // we are a deletion
-            return basesAreRepeated(ref.getBaseString(), alt.getBaseString(), refBasesStartingAtVCWithoutPad, 2);
-        } else { // we are an insertion
-            return basesAreRepeated(alt.getBaseString(), ref.getBaseString(), refBasesStartingAtVCWithoutPad, 1);
-        }
-    }
-    
-    protected static boolean basesAreRepeated(final String l, final String s, final String ref, final int minNumberOfMatches) {
-        final String potentialRepeat = l.substring(s.length()); // skip s bases
-        
-        for ( int i = 0; i < minNumberOfMatches; i++) {
-            final int start = i * potentialRepeat.length();
-            final int end = (i+1) * potentialRepeat.length();
-            if ( ref.length() < end )
-                 return false; // we ran out of bases to test
-            final String refSub = ref.substring(start, end);
-            if ( ! refSub.equals(potentialRepeat) )
-                return false; // repeat didn't match, fail
-        }
-
-        return true; // we passed all tests, we matched
-    }
-
     /**
      * Compute the end position for this VariantContext from the alleles themselves
      *
@@ -1368,11 +1005,11 @@ public class VariantContextUtils {
         final Allele ref = alleles.get(0);
 
         if ( ref.isNonReference() )
-            throw new ReviewedStingException("computeEndFromAlleles requires first allele to be reference");
+            throw new IllegalStateException("computeEndFromAlleles requires first allele to be reference");
 
         if ( VariantContext.hasSymbolicAlleles(alleles) ) {
             if ( endForSymbolicAlleles == -1 )
-                throw new ReviewedStingException("computeEndFromAlleles found a symbolic allele but endForSymbolicAlleles was provided");
+                throw new IllegalStateException("computeEndFromAlleles found a symbolic allele but endForSymbolicAlleles was provided");
             return endForSymbolicAlleles;
         } else {
             return start + Math.max(ref.length() - 1, 0);
@@ -1408,80 +1045,4 @@ public class VariantContextUtils {
         }
     }
 
-    public static VariantContext reverseTrimAlleles( final VariantContext inputVC ) {
-
-        // see whether we need to trim common reference base from all alleles
-        final int trimExtent = computeReverseClipping(inputVC.getAlleles(), inputVC.getReference().getDisplayString().getBytes(), 0, false);
-        if ( trimExtent <= 0 || inputVC.getAlleles().size() <= 1 )
-            return inputVC;
-
-        final List<Allele> alleles = new ArrayList<Allele>();
-        final GenotypesContext genotypes = GenotypesContext.create();
-        final Map<Allele, Allele> originalToTrimmedAlleleMap = new HashMap<Allele, Allele>();
-
-        for (final Allele a : inputVC.getAlleles()) {
-            if (a.isSymbolic()) {
-                alleles.add(a);
-                originalToTrimmedAlleleMap.put(a, a);
-            } else {
-                // get bases for current allele and create a new one with trimmed bases
-                final byte[] newBases = Arrays.copyOfRange(a.getBases(), 0, a.length()-trimExtent);
-                final Allele trimmedAllele = Allele.create(newBases, a.isReference());
-                alleles.add(trimmedAllele);
-                originalToTrimmedAlleleMap.put(a, trimmedAllele);
-            }
-        }
-
-        // now we can recreate new genotypes with trimmed alleles
-        for ( final Genotype genotype : inputVC.getGenotypes() ) {
-            final List<Allele> originalAlleles = genotype.getAlleles();
-            final List<Allele> trimmedAlleles = new ArrayList<Allele>();
-            for ( final Allele a : originalAlleles ) {
-                if ( a.isCalled() )
-                    trimmedAlleles.add(originalToTrimmedAlleleMap.get(a));
-                else
-                    trimmedAlleles.add(Allele.NO_CALL);
-            }
-            genotypes.add(new GenotypeBuilder(genotype).alleles(trimmedAlleles).make());
-        }
-
-        return new VariantContextBuilder(inputVC).stop(inputVC.getStart() + alleles.get(0).length() - 1).alleles(alleles).genotypes(genotypes).make();
-    }
-
-    public static int computeReverseClipping(final List<Allele> unclippedAlleles,
-                                             final byte[] ref,
-                                             final int forwardClipping,
-                                             final boolean allowFullClip) {
-        int clipping = 0;
-        boolean stillClipping = true;
-
-        while ( stillClipping ) {
-            for ( final Allele a : unclippedAlleles ) {
-                if ( a.isSymbolic() )
-                    continue;
-
-                // we need to ensure that we don't reverse clip out all of the bases from an allele because we then will have the wrong
-                // position set for the VariantContext (although it's okay to forward clip it all out, because the position will be fine).
-                if ( a.length() - clipping == 0 )
-                    return clipping - (allowFullClip ? 0 : 1);
-
-                if ( a.length() - clipping <= forwardClipping || a.length() - forwardClipping == 0 ) {
-                    stillClipping = false;
-                }
-                else if ( ref.length == clipping ) {
-                    if ( allowFullClip )
-                        stillClipping = false;
-                    else
-                        return -1;
-                }
-                else if ( a.getBases()[a.length()-clipping-1] != ref[ref.length-clipping-1] ) {
-                    stillClipping = false;
-                }
-            }
-            if ( stillClipping )
-                clipping++;
-        }
-
-        return clipping;
-    }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java b/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java
index abe85e383..96643b9e9 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContext.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/VariantJEXLContext.java
@@ -21,13 +21,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import org.apache.commons.jexl2.JexlContext;
 import org.apache.commons.jexl2.MapContext;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broadinstitute.variant.utils.Utils;
+import org.broadinstitute.variant.vcf.VCFConstants;
 
 import java.util.Collection;
 import java.util.HashMap;
@@ -275,7 +274,7 @@ class JEXLMap implements Map<VariantContextUtils.JexlVCMatchExp, Boolean> {
             if (e.getMessage().contains("undefined variable"))
                 jexl.put(exp,false);
             else
-                throw new UserException.CommandLineException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
+                throw new IllegalArgumentException(String.format("Invalid JEXL expression detected for %s with message %s", exp.name, e.getMessage()));
         }
     }
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Encoder.java
similarity index 93%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Encoder.java
index 22acc4787..f71f4e577 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Encoder.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Encoder.java
@@ -22,13 +22,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.variant.bcf2.BCF2Type;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
 
 import java.io.ByteArrayOutputStream;
 import java.io.IOException;
@@ -80,7 +79,7 @@ public final class BCF2Encoder {
                 case INT32: encodeTypedInt((Integer)value, type); break;
                 case FLOAT: encodeTypedFloat((Double) value); break;
                 case CHAR:  encodeTypedString((String) value); break;
-                default:    throw new ReviewedStingException("Illegal type encountered " + type);
+                default:    throw new IllegalArgumentException("Illegal type encountered " + type);
             }
         }
     }
@@ -155,7 +154,7 @@ public final class BCF2Encoder {
                     case INT32: encodeRawBytes((Integer) value, type); break;
                     case FLOAT: encodeRawFloat((Double) value); break;
                     case CHAR:  encodeRawChar((Byte) value); break;
-                    default:    throw new ReviewedStingException("Illegal type encountered " + type);
+                    default:    throw new IllegalArgumentException("Illegal type encountered " + type);
                 }
             }
         } catch ( ClassCastException e ) {
@@ -238,7 +237,7 @@ public final class BCF2Encoder {
      */
     @Requires("o != null")
     public final BCF2Type encode(final Object o) throws IOException {
-        if ( o == null ) throw new ReviewedStingException("Generic encode cannot deal with null values");
+        if ( o == null ) throw new IllegalArgumentException("Generic encode cannot deal with null values");
 
         if ( o instanceof List ) {
             final BCF2Type type = determineBCFType(((List) o).get(0));
@@ -262,7 +261,7 @@ public final class BCF2Encoder {
         else if ( toType instanceof Double )
             return BCF2Type.FLOAT;
         else
-            throw new ReviewedStingException("No native encoding for Object of type " + arg.getClass().getSimpleName());
+            throw new IllegalArgumentException("No native encoding for Object of type " + arg.getClass().getSimpleName());
     }
 
     private final List<Byte> stringToBytes(final String v) throws IOException {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldEncoder.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldEncoder.java
index a91eb216d..5f3e66c2a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldEncoder.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldEncoder.java
@@ -22,17 +22,16 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Invariant;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCompoundHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineCount;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.bcf2.BCF2Type;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
+import org.broadinstitute.variant.vcf.VCFCompoundHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderLineCount;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.IOException;
 import java.util.Collections;
@@ -85,7 +84,7 @@ public abstract class BCF2FieldEncoder {
         this.staticType = staticType;
 
         final Integer offset = dict.get(getField());
-        if ( offset == null ) throw new ReviewedStingException("Format error: could not find string " + getField() + " in header as required by BCF");
+        if ( offset == null ) throw new IllegalStateException("Format error: could not find string " + getField() + " in header as required by BCF");
         this.dictionaryOffset = offset;
         dictionaryOffsetType = BCF2Utils.determineIntegerType(offset);
     }
@@ -260,7 +259,7 @@ public abstract class BCF2FieldEncoder {
     @Requires("isDynamicallyTyped()")
     @Ensures("result != null")
     public BCF2Type getDynamicType(final Object value) {
-        throw new ReviewedStingException("BUG: cannot get dynamic type for statically typed BCF2 field " + getField());
+        throw new IllegalStateException("BUG: cannot get dynamic type for statically typed BCF2 field " + getField());
     }
 
     // ----------------------------------------------------------------------
@@ -351,7 +350,7 @@ public abstract class BCF2FieldEncoder {
         public Flag(final VCFCompoundHeaderLine headerLine, final Map<String, Integer> dict ) {
             super(headerLine, dict, BCF2Type.INT8);
             if ( ! headerLine.isFixedCount() || headerLine.getCount() != 0 )
-                throw new ReviewedStingException("Flag encoder only suppports atomic flags for field " + getField());
+                throw new IllegalStateException("Flag encoder only supports atomic flags for field " + getField());
         }
 
         @Override
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriter.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriter.java
index 61c0129bb..c75242e8b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriter.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriter.java
@@ -22,17 +22,16 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.bcf2.BCF2Type;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.Genotype;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.IOException;
 import java.util.ArrayList;
@@ -208,7 +207,7 @@ public abstract class BCF2FieldWriter {
             this.ige = ige;
 
             if ( ! (fieldEncoder instanceof BCF2FieldEncoder.IntArray) )
-                throw new ReviewedStingException("BUG: IntGenotypesWriter requires IntArray encoder for field " + getField());
+                throw new IllegalArgumentException("BUG: IntGenotypesWriter requires IntArray encoder for field " + getField());
         }
 
         @Override
@@ -266,7 +265,7 @@ public abstract class BCF2FieldWriter {
         @Override
         public void start(final BCF2Encoder encoder, final VariantContext vc) throws IOException {
             if ( vc.getNAlleles() > BCF2Utils.MAX_ALLELES_IN_GENOTYPES )
-                throw new ReviewedStingException("Current BCF2 encoder cannot handle sites " +
+                throw new IllegalStateException("Current BCF2 encoder cannot handle sites " +
                         "with > " + BCF2Utils.MAX_ALLELES_IN_GENOTYPES + " alleles, but you have "
                         + vc.getNAlleles() + " at " + vc.getChr() + ":" + vc.getStart());
 
@@ -312,7 +311,7 @@ public abstract class BCF2FieldWriter {
             else if ( a == Allele.NO_CALL ) return -1;
             else {
                 final Integer o = alleleMapForTriPlus.get(a);
-                if ( o == null ) throw new ReviewedStingException("BUG: Couldn't find allele offset for allele " + a);
+                if ( o == null ) throw new IllegalStateException("BUG: Couldn't find allele offset for allele " + a);
                 return o;
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java
index 9c63a69e7..e8d58f2f2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2FieldWriterManager.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2FieldWriterManager.java
@@ -22,13 +22,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broadinstitute.variant.vcf.*;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -74,7 +73,7 @@ public class BCF2FieldWriterManager {
     @Ensures("map.containsKey(field)")
     private final <T> void add(final Map<String, T> map, final String field, final T writer) {
         if ( map.containsKey(field) )
-            throw new ReviewedStingException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders");
+            throw new IllegalStateException("BUG: field " + field + " already seen in VCFHeader while building BCF2 field encoders");
         map.put(field, writer);
     }
 
@@ -118,7 +117,7 @@ public class BCF2FieldWriterManager {
                     else
                         return new BCF2FieldEncoder.GenericInts(line, dict);
                 default:
-                    throw new ReviewedStingException("Unexpected type for field " + line.getID());
+                    throw new IllegalArgumentException("Unexpected type for field " + line.getID());
             }
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java
similarity index 91%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java
index 536f07f90..3e37ade25 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/BCF2Writer.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/BCF2Writer.java
@@ -22,23 +22,21 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Type;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCFVersion;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFContigHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.bcf2.BCF2Codec;
+import org.broadinstitute.variant.bcf2.BCF2Type;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
+import org.broadinstitute.variant.bcf2.BCFVersion;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.vcf.VCFContigHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.*;
+import org.broadinstitute.variant.vcf.VCFUtils;
 
 import java.io.*;
 import java.util.*;
@@ -133,7 +131,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
                 logger.warn("No contig dictionary found in header, falling back to reference sequence dictionary");
                 createContigDictionary(VCFUtils.makeContigHeaderLines(getRefDict(), null));
             } else {
-                throw new UserException.MalformedBCF2("Cannot write BCF2 file with missing contig lines");
+                throw new IllegalStateException("Cannot write BCF2 file with missing contig lines");
             }
         } else {
             createContigDictionary(header.getContigLines());
@@ -163,7 +161,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
             BCF2Type.INT32.write(headerBytes.length, outputStream);
             outputStream.write(headerBytes);
         } catch (IOException e) {
-            throw new UserException.CouldNotCreateOutputFile("BCF2 stream", "Got IOException while trying to write BCF2 header", e);
+            throw new RuntimeException("BCF2 stream: Got IOException while trying to write BCF2 header", e);
         }
     }
 
@@ -183,7 +181,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
             writeBlock(infoBlock, genotypesBlock);
         }
         catch ( IOException e ) {
-            throw new UserException("Error writing record to BCF2 file: " + vc.toString(), e);
+            throw new RuntimeException("Error writing record to BCF2 file: " + vc.toString(), e);
         }
     }
 
@@ -194,7 +192,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
             outputStream.close();
         }
         catch ( IOException e ) {
-            throw new UserException("Failed to close BCF2 file");
+            throw new RuntimeException("Failed to close BCF2 file");
         }
         super.close();
     }
@@ -214,7 +212,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
     private byte[] buildSitesData( VariantContext vc ) throws IOException {
         final int contigIndex = contigDictionary.get(vc.getChr());
         if ( contigIndex == -1 )
-            throw new UserException(String.format("Contig %s not found in sequence dictionary from reference", vc.getChr()));
+            throw new IllegalStateException(String.format("Contig %s not found in sequence dictionary from reference", vc.getChr()));
 
         // note use of encodeRawValue to not insert the typing byte
         encoder.encodeRawValue(contigIndex, BCF2Type.INT32);
@@ -309,7 +307,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
         for ( Allele allele : vc.getAlleles() ) {
             final byte[] s = allele.getDisplayBases();
             if ( s == null )
-                throw new ReviewedStingException("BUG: BCF2Writer encountered null padded allele" + allele);
+                throw new IllegalStateException("BUG: BCF2Writer encountered null padded allele" + allele);
             encoder.encodeTypedString(s);
         }
     }
@@ -370,7 +368,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
      * @param fieldType
      */
     private final void errorUnexpectedFieldToWrite(final VariantContext vc, final String field, final String fieldType) {
-        throw new UserException("Found field " + field + " in the " + fieldType + " fields of VariantContext at " +
+        throw new IllegalStateException("Found field " + field + " in the " + fieldType + " fields of VariantContext at " +
                 vc.getChr() + ":" + vc.getStart() + " from " + vc.getSource() + " but this hasn't been defined in the VCFHeader");
     }
 
@@ -403,7 +401,7 @@ class BCF2Writer extends IndexingVariantContextWriter {
         // iterate over strings until we find one that needs 16 bits, and break
         for ( final String string : strings ) {
             final Integer got = stringDictionaryMap.get(string);
-            if ( got == null ) throw new ReviewedStingException("Format error: could not find string " + string + " in header as required by BCF");
+            if ( got == null ) throw new IllegalStateException("Format error: could not find string " + string + " in header as required by BCF");
             final int offset = got;
             offsets.add(offset);
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java
similarity index 85%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java
index 298f12da3..6311d9e9a 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IndexingVariantContextWriter.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IndexingVariantContextWriter.java
@@ -22,21 +22,19 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import net.sf.samtools.SAMSequenceDictionary;
+import net.sf.samtools.SAMSequenceRecord;
 import org.broad.tribble.Tribble;
 import org.broad.tribble.index.DynamicIndexCreator;
 import org.broad.tribble.index.Index;
 import org.broad.tribble.index.IndexFactory;
 import org.broad.tribble.util.LittleEndianOutputStream;
-import org.broadinstitute.sting.gatk.refdata.tracks.IndexDictionaryUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.*;
 
@@ -97,7 +95,7 @@ abstract class IndexingVariantContextWriter implements VariantContextWriter {
             // try to close the index stream (keep it separate to help debugging efforts)
             if ( indexer != null ) {
                 Index index = indexer.finalizeIndex(positionalOutputStream.getPosition());
-                IndexDictionaryUtils.setIndexSequenceDictionary(index, refDict);
+                setIndexSequenceDictionary(index, refDict);
                 index.write(idxStream);
                 idxStream.close();
             }
@@ -105,7 +103,7 @@ abstract class IndexingVariantContextWriter implements VariantContextWriter {
             // close the underlying output stream as well
             outputStream.close();
         } catch (IOException e) {
-            throw new ReviewedStingException("Unable to close index for " + getStreamName(), e);
+            throw new RuntimeException("Unable to close index for " + getStreamName(), e);
         }
     }
 
@@ -137,6 +135,17 @@ abstract class IndexingVariantContextWriter implements VariantContextWriter {
     protected static final String writerName(final File location, final OutputStream stream) {
         return location == null ? stream.toString() : location.getAbsolutePath();
     }
+
+    // a constant we use for marking sequence dictionary entries in the Tribble index property list
+    private static final String SequenceDictionaryPropertyPredicate = "DICT:";
+
+    private static void setIndexSequenceDictionary(Index index, SAMSequenceDictionary dict) {
+        for ( SAMSequenceRecord seq : dict.getSequences() ) {
+            final String contig = SequenceDictionaryPropertyPredicate + seq.getSequenceName();
+            final String length = String.valueOf(seq.getSequenceLength());
+            index.addProperty(contig,length);
+        }
+    }
 }
 
 final class PositionalOutputStream extends OutputStream {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
index fc117e5e1..e1d07d6f7 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/IntGenotypeFieldAccessors.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/IntGenotypeFieldAccessors.java
@@ -22,10 +22,10 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.variantcontext.Genotype;
 
 import java.util.HashMap;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/Options.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/Options.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/Options.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/Options.java
index 3a5cb23b0..7aa7fb123 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/Options.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/Options.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 /**
  * Available writer options for VariantContextWriters
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriter.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriter.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriter.java
index b51892b31..4de130514 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriter.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriter.java
@@ -23,9 +23,9 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * this class writes VCF files, allowing records to be passed in unsorted (up to a certain genomic distance away)
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriterBase.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriterBase.java
index 1f3cdd0fe..413afa0fd 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/SortingVariantContextWriterBase.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/SortingVariantContextWriterBase.java
@@ -23,10 +23,10 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.*;
 import java.util.concurrent.PriorityBlockingQueue;
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java
index 4c35d6181..175434853 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriter.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VCFWriter.java
@@ -22,15 +22,13 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.vcf.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.*;
 import java.lang.reflect.Array;
@@ -119,7 +117,7 @@ class VCFWriter extends IndexingVariantContextWriter {
             mHeader = writeHeader(header, writer, doNotWriteGenotypes, getVersionLine(), getStreamName());
             flushBuffer();
         } catch ( IOException e ) {
-            throw new UserException.CouldNotCreateOutputFile(getStreamName(), e);
+            throw new RuntimeException("Couldn't write file " + getStreamName(), e);
         }
     }
 
@@ -171,7 +169,7 @@ class VCFWriter extends IndexingVariantContextWriter {
             writer.flush();  // necessary so that writing to an output stream will work
         }
         catch (IOException e) {
-            throw new ReviewedStingException("IOException writing the VCF header to " + streamNameForError, e);
+            throw new RuntimeException("IOException writing the VCF header to " + streamNameForError, e);
         }
 
         return header;
@@ -187,7 +185,7 @@ class VCFWriter extends IndexingVariantContextWriter {
             // TODO -- would it be useful to null out the line buffer so we don't have it around unnecessarily?
             writer.close();
         } catch (IOException e) {
-            throw new ReviewedStingException("Unable to close " + getStreamName(), e);
+            throw new RuntimeException("Unable to close " + getStreamName(), e);
         }
 
         super.close();
@@ -398,7 +396,7 @@ class VCFWriter extends IndexingVariantContextWriter {
             for ( String field : genotypeFormatKeys ) {
                 if ( field.equals(VCFConstants.GENOTYPE_KEY) ) {
                     if ( !g.isAvailable() ) {
-                        throw new ReviewedStingException("GTs cannot be missing for some samples if they are available for others in the record");
+                        throw new IllegalStateException("GTs cannot be missing for some samples if they are available for others in the record");
                     }
 
                     writeAllele(g.getAllele(0), alleleMap);
@@ -599,10 +597,9 @@ class VCFWriter extends IndexingVariantContextWriter {
 
     private final void fieldIsMissingFromHeaderError(final VariantContext vc, final String id, final String field) {
         if ( !allowMissingFieldsInHeader)
-            throw new UserException.MalformedVCFHeader("Key " + id + " found in VariantContext field " + field
+            throw new IllegalStateException("Key " + id + " found in VariantContext field " + field
                     + " at " + vc.getChr() + ":" + vc.getStart()
-                    + " but this key isn't defined in the VCFHeader.  The GATK now requires all VCFs to have"
-                    + " complete VCF headers by default.  This error can be disabled with the engine argument"
-                    + " -U LENIENT_VCF_PROCESSING");
+                    + " but this key isn't defined in the VCFHeader.  We require all VCFs to have"
+                    + " complete VCF headers by default.");
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriter.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriter.java
similarity index 56%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriter.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriter.java
index 0ad78c7e0..4313b044d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriter.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriter.java
@@ -1,7 +1,7 @@
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 /**
  * this class writes VCF files
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
similarity index 93%
rename from public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java
rename to public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
index 035aff7d6..0c98567a1 100644
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWriterFactory.java
+++ b/public/java/src/org/broadinstitute/variant/variantcontext/writer/VariantContextWriterFactory.java
@@ -22,10 +22,9 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import net.sf.samtools.SAMSequenceDictionary;
-import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -107,7 +106,7 @@ public class VariantContextWriterFactory {
     }
 
     /**
-     * Returns a output stream writing to location, or throws a UserException if this fails
+     * Returns a output stream writing to location, or throws an exception if this fails
      * @param location
      * @return
      */
@@ -115,7 +114,7 @@ public class VariantContextWriterFactory {
         try {
             return new FileOutputStream(location);
         } catch (FileNotFoundException e) {
-            throw new UserException.CouldNotCreateOutputFile(location, "Unable to create VCF writer", e);
+            throw new RuntimeException(location + ": Unable to create VCF writer", e);
         }
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
rename to public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
index 652f7f96f..3bad6b064 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/AbstractVCFCodec.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/AbstractVCFCodec.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.apache.log4j.Logger;
 import org.broad.tribble.AsciiFeatureCodec;
@@ -8,9 +8,7 @@ import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
 import org.broad.tribble.util.BlockCompressedInputStream;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 
 import java.io.FileInputStream;
 import java.io.FileNotFoundException;
@@ -148,7 +146,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
                     sampleNames.add(strings[arrayIndex++]);
 
                 if ( sawFormatTag && sampleNames.size() == 0 )
-                    throw new UserException.MalformedVCFHeader("The FORMAT field was provided but there is no genotype/sample data");
+                    throw new TribbleException.InvalidHeader("The FORMAT field was provided but there is no genotype/sample data");
 
             } else {
                 if ( str.startsWith(VCFConstants.INFO_HEADER_START) ) {
@@ -203,7 +201,7 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
         if (line.startsWith(VCFHeader.HEADER_INDICATOR)) return null;
 
         // our header cannot be null, we need the genotype sample names and counts
-        if (header == null) throw new ReviewedStingException("VCF Header cannot be null when decoding a record");
+        if (header == null) throw new TribbleException("VCF Header cannot be null when decoding a record");
 
         if (parts == null)
             parts = new String[Math.min(header.getColumnCount(), NUM_STANDARD_FIELDS+1)];
@@ -213,8 +211,8 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
         // if we have don't have a header, or we have a header with no genotyping data check that we have eight columns.  Otherwise check that we have nine (normal colummns + genotyping data)
         if (( (header == null || !header.hasGenotypingData()) && nParts != NUM_STANDARD_FIELDS) ||
                 (header != null && header.hasGenotypingData() && nParts != (NUM_STANDARD_FIELDS + 1)) )
-            throw new UserException.MalformedVCF("there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
-                    " tokens, and saw " + nParts + " )", lineNo);
+            throw new TribbleException("Line " + lineNo + ": there aren't enough columns for line " + line + " (we expected " + (header == null ? NUM_STANDARD_FIELDS : NUM_STANDARD_FIELDS + 1) +
+                    " tokens, and saw " + nParts + " )");
 
         return parseVCFLine(parts, includeGenotypes);
     }
@@ -692,10 +690,10 @@ public abstract class AbstractVCFCodec extends AsciiFeatureCodec<VariantContext>
 
 
     protected void generateException(String message) {
-        throw new UserException.MalformedVCF(message, lineNo);
+        throw new TribbleException(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
     }
 
     protected static void generateException(String message, int lineNo) {
-        throw new UserException.MalformedVCF(message, lineNo);
+        throw new TribbleException(String.format("The provided VCF file is malformed at approximately line number %d: %s", lineNo, message));
     }
 }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java b/public/java/src/org/broadinstitute/variant/vcf/VCF3Codec.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCF3Codec.java
index 2c103b473..6cbd26de9 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCF3Codec.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCF3Codec.java
@@ -22,12 +22,10 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
-import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.variantcontext.*;
 
 import java.io.IOException;
 import java.util.*;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java b/public/java/src/org/broadinstitute/variant/vcf/VCFCodec.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFCodec.java
index f12f13dc7..6a31727ee 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCodec.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFCodec.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broad.tribble.TribbleException;
 import org.broad.tribble.readers.LineReader;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java
index 5273806a7..68252f01b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFCompoundHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFCompoundHeaderLine.java
@@ -22,14 +22,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.apache.log4j.Logger;
 import org.broad.tribble.TribbleException;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.GenotypeLikelihoods;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.GenotypeLikelihoods;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.util.Arrays;
 import java.util.LinkedHashMap;
@@ -65,7 +63,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
     public boolean isFixedCount() { return countType == VCFHeaderLineCount.INTEGER; }
     public int getCount() {
         if ( ! isFixedCount() )
-            throw new ReviewedStingException("Asking for header line count when type is not an integer");
+            throw new TribbleException("Asking for header line count when type is not an integer");
         return count;
     }
 
@@ -91,7 +89,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
                 final int ploidy = vc.getMaxPloidy(2);
                 return GenotypeLikelihoods.numLikelihoods(vc.getNAlleles(), ploidy);
             default:
-                throw new ReviewedStingException("Unknown count type: " + countType);
+                throw new TribbleException("Unknown count type: " + countType);
         }
     }
 
@@ -172,7 +170,7 @@ public abstract class VCFCompoundHeaderLine extends VCFHeaderLine implements VCF
         }
 
         if ( count < 0 && countType == VCFHeaderLineCount.INTEGER )
-            throw new UserException.MalformedVCFHeader("Count < 0 for fixed size VCF header field " + name);
+            throw new TribbleException.InvalidHeader("Count < 0 for fixed size VCF header field " + name);
 
         try {
             type = VCFHeaderLineType.valueOf(mapping.get("Type"));
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java b/public/java/src/org/broadinstitute/variant/vcf/VCFConstants.java
similarity index 99%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFConstants.java
index dac58eb10..09e74cff6 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFConstants.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFConstants.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import java.util.Locale;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java
index 35cc75af2..f4bcd69bf 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFContigHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFContigHeaderLine.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import java.util.Map;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFFilterHeaderLine.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFFilterHeaderLine.java
index bfc484a7e..ff5352404 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFilterHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFFilterHeaderLine.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import java.util.Arrays;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFFormatHeaderLine.java
similarity index 95%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFFormatHeaderLine.java
index 5fc3187c5..5d749f37d 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFFormatHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFFormatHeaderLine.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java
similarity index 97%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java
index 44a3e9af3..46f9187a1 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeader.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeader.java
@@ -22,11 +22,11 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.apache.log4j.Logger;
+import org.broad.tribble.TribbleException;
 import org.broad.tribble.util.ParsingUtils;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -124,7 +124,7 @@ public class VCFHeader {
         this(metaData);
 
         if ( genotypeSampleNames.size() != new HashSet<String>(genotypeSampleNames).size() )
-            throw new ReviewedStingException("BUG: VCF header has duplicate sample names");
+            throw new TribbleException.InvalidHeader("BUG: VCF header has duplicate sample names");
 
         mGenotypeSampleNames.addAll(genotypeSampleNames);
         samplesWereAlreadySorted = ParsingUtils.isSorted(genotypeSampleNames);
@@ -234,7 +234,7 @@ public class VCFHeader {
 
         if ( hasFormatLine(VCFConstants.GENOTYPE_LIKELIHOODS_KEY) && ! hasFormatLine(VCFConstants.GENOTYPE_PL_KEY) ) {
             logger.warn("Found " + VCFConstants.GENOTYPE_LIKELIHOODS_KEY + " format, but no "
-                    + VCFConstants.GENOTYPE_PL_KEY + " field.  As the GATK now only manages PL fields internally"
+                    + VCFConstants.GENOTYPE_PL_KEY + " field.  We now only manage PL fields internally"
                     + " automatically adding a corresponding PL field to your VCF header");
             addMetaDataLine(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_PL_KEY, VCFHeaderLineCount.G, VCFHeaderLineType.Integer, "Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification"));
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLine.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLine.java
index 9b5886c65..3333fd455 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLine.java
@@ -23,7 +23,7 @@
  * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broad.tribble.TribbleException;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineCount.java
similarity index 72%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineCount.java
index d615c7c78..2bef149a2 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineCount.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineCount.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 /**
  * the count encodings we use for fields in VCF header lines
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineTranslator.java
similarity index 93%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineTranslator.java
index dcc38a6f9..1b20c52ff 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineTranslator.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineTranslator.java
@@ -1,6 +1,6 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
-import org.broadinstitute.sting.utils.exceptions.UserException;
+import org.broad.tribble.TribbleException;
 
 import java.util.*;
 
@@ -77,10 +77,10 @@ class VCF4Parser implements VCFLineParser {
         index = 0;
         if ( expectedTagOrder != null ) {
             if ( ret.size() > expectedTagOrder.size() )
-                throw new UserException.MalformedVCFHeader("unexpected tag count " + ret.size() + " in line " + valueLine);
+                throw new TribbleException.InvalidHeader("unexpected tag count " + ret.size() + " in line " + valueLine);
             for ( String str : ret.keySet() ) {
                 if ( !expectedTagOrder.get(index).equals(str) )
-                    throw new UserException.MalformedVCFHeader("Unexpected tag " + str + " in line " + valueLine);
+                    throw new TribbleException.InvalidHeader("Unexpected tag " + str + " in line " + valueLine);
                 index++;
             }
         }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineType.java
similarity index 74%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineType.java
index 83e272415..0defd09c5 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderLineType.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderLineType.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 /**
  * the type encodings we use for fields in VCF header lines
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderVersion.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFHeaderVersion.java
index c65ce17b9..16229857e 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderVersion.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFHeaderVersion.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broad.tribble.TribbleException;
 
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFIDHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFIDHeaderLine.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFIDHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFIDHeaderLine.java
index 65321881a..c18c1b6ea 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFIDHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFIDHeaderLine.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 /** an interface for ID-based header lines **/
 public interface VCFIDHeaderLine {
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFInfoHeaderLine.java
similarity index 94%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFInfoHeaderLine.java
index 9f249c531..7db527efe 100755
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFInfoHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFInfoHeaderLine.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 
 /**
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java b/public/java/src/org/broadinstitute/variant/vcf/VCFSimpleHeaderLine.java
similarity index 98%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFSimpleHeaderLine.java
index c9699e7b5..94a1bd20b 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFSimpleHeaderLine.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFSimpleHeaderLine.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import java.util.LinkedHashMap;
 import java.util.List;
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java b/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java
similarity index 96%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java
index b2e8cc100..5b00cfa37 100644
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLines.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFStandardHeaderLines.java
@@ -22,12 +22,12 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import com.google.java.contract.Ensures;
 import com.google.java.contract.Requires;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
+import org.broad.tribble.TribbleException;
 
 import java.util.*;
 
@@ -76,7 +76,7 @@ public class VCFStandardHeaderLines {
     /**
      * Adds header lines for each of the format fields in IDs to header, returning the set of
      * IDs without standard descriptions, unless throwErrorForMissing is true, in which
-     * case this situation results in a ReviewedStingException
+     * case this situation results in a TribbleException
      *
      * @param IDs
      * @return
@@ -126,7 +126,7 @@ public class VCFStandardHeaderLines {
     /**
      * Adds header lines for each of the info fields in IDs to header, returning the set of
      * IDs without standard descriptions, unless throwErrorForMissing is true, in which
-     * case this situation results in a ReviewedStingException
+     * case this situation results in a TribbleException
      *
      * @param IDs
      * @return
@@ -246,7 +246,7 @@ public class VCFStandardHeaderLines {
         @Ensures({"standards.containsKey(line.getID())"})
         public void add(final T line) {
             if ( standards.containsKey(line.getID()) )
-                throw new ReviewedStingException("Attempting to add multiple standard header lines for ID " + line.getID());
+                throw new TribbleException("Attempting to add multiple standard header lines for ID " + line.getID());
             standards.put(line.getID(), line);
         }
 
@@ -255,7 +255,7 @@ public class VCFStandardHeaderLines {
         public T get(final String ID, final boolean throwErrorForMissing) {
             final T x = standards.get(ID);
             if ( throwErrorForMissing && x == null )
-                throw new ReviewedStingException("Couldn't find a standard VCF header line for field " + ID);
+                throw new TribbleException("Couldn't find a standard VCF header line for field " + ID);
             return x;
         }
     }
diff --git a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java b/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java
old mode 100755
new mode 100644
similarity index 57%
rename from public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
rename to public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java
index a8aefb703..ccb9935cb
--- a/public/java/src/org/broadinstitute/sting/utils/codecs/vcf/VCFUtils.java
+++ b/public/java/src/org/broadinstitute/variant/vcf/VCFUtils.java
@@ -1,160 +1,15 @@
-/*
- * Copyright (c) 2010 The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
- * THE USE OR OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.commons.io.FilenameUtils;
 import org.apache.log4j.Logger;
-import org.broad.tribble.Feature;
-import org.broad.tribble.FeatureCodecHeader;
-import org.broad.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.commandline.RodBinding;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 
 import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
 import java.util.*;
 
-/**
- * A set of static utility methods for common operations on VCF files/records.
- */
 public class VCFUtils {
-    /**
-     * Constructor access disallowed...static utility methods only!
-     */
-    private VCFUtils() { }
-
-    public static <T extends Feature> Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, List<RodBinding<T>> rodBindings) {
-        // Collect the eval rod names
-        final Set<String> names = new TreeSet<String>();
-        for ( final RodBinding<T> evalRod : rodBindings )
-            names.add(evalRod.getName());
-        return getVCFHeadersFromRods(toolkit, names);
-    }
-
-    public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit) {
-        return getVCFHeadersFromRods(toolkit, (Collection<String>)null);
-    }
-
-    public static Map<String, VCFHeader> getVCFHeadersFromRods(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
-        Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
-
-        // iterate to get all of the sample names
-        List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
-        for ( ReferenceOrderedDataSource source : dataSources ) {
-            // ignore the rod if it's not in our list
-            if ( rodNames != null && !rodNames.contains(source.getName()) )
-                continue;
-
-            if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader )
-                data.put(source.getName(), (VCFHeader)source.getHeader());
-        }
-
-        return data;
-    }
-
-    public static Map<String,VCFHeader> getVCFHeadersFromRodPrefix(GenomeAnalysisEngine toolkit,String prefix) {
-        Map<String, VCFHeader> data = new HashMap<String, VCFHeader>();
-
-        // iterate to get all of the sample names
-        List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
-        for ( ReferenceOrderedDataSource source : dataSources ) {
-            // ignore the rod if lacks the prefix
-            if ( ! source.getName().startsWith(prefix) )
-                continue;
-
-            if ( source.getHeader() != null && source.getHeader() instanceof VCFHeader )
-                data.put(source.getName(), (VCFHeader)source.getHeader());
-        }
-
-        return data;
-    }
-
-    /**
-     * Gets the header fields from all VCF rods input by the user
-     *
-     * @param toolkit    GATK engine
-     *
-     * @return a set of all fields
-     */
-    public static Set<VCFHeaderLine> getHeaderFields(GenomeAnalysisEngine toolkit) {
-        return getHeaderFields(toolkit, null);
-    }
-
-    /**
-     * Gets the header fields from all VCF rods input by the user
-     *
-     * @param toolkit    GATK engine
-     * @param rodNames   names of rods to use, or null if we should use all possible ones
-     *
-     * @return a set of all fields
-     */
-    public static Set<VCFHeaderLine> getHeaderFields(GenomeAnalysisEngine toolkit, Collection<String> rodNames) {
-
-        // keep a map of sample name to occurrences encountered
-        TreeSet<VCFHeaderLine> fields = new TreeSet<VCFHeaderLine>();
-
-        // iterate to get all of the sample names
-        List<ReferenceOrderedDataSource> dataSources = toolkit.getRodDataSources();
-        for ( ReferenceOrderedDataSource source : dataSources ) {
-            // ignore the rod if it's not in our list
-            if ( rodNames != null && !rodNames.contains(source.getName()) )
-                continue;
-
-            if ( source.getRecordType().equals(VariantContext.class)) {
-                VCFHeader header = (VCFHeader)source.getHeader();
-                if ( header != null )
-                    fields.addAll(header.getMetaDataInSortedOrder());
-            }
-        }
-
-        return fields;
-    }
-
-    /** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */
-    private static final class HeaderConflictWarner {
-        Logger logger;
-        Set<String> alreadyIssued = new HashSet<String>();
-
-        private HeaderConflictWarner(final Logger logger) {
-            this.logger = logger;
-        }
-
-        public void warn(final VCFHeaderLine line, final String msg) {
-            if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) {
-                alreadyIssued.add(line.getKey());
-                logger.warn(msg);
-            }
-        }
-    }
 
     public static Set<VCFHeaderLine> smartMergeHeaders(Collection<VCFHeader> headers, Logger logger) throws IllegalStateException {
         HashMap<String, VCFHeaderLine> map = new HashMap<String, VCFHeaderLine>(); // from KEY.NAME -> line
@@ -236,16 +91,6 @@ public class VCFUtils {
         return rsID;
     }
 
-    /**
-     * Add / replace the contig header lines in the VCFHeader with the information in the GATK engine
-     *
-     * @param header the header to update
-     * @param engine the GATK engine containing command line arguments and the master sequence dictionary
-     */
-    public static VCFHeader withUpdatedContigs(final VCFHeader header, final GenomeAnalysisEngine engine) {
-        return VCFUtils.withUpdatedContigs(header, engine.getArguments().referenceFile, engine.getMasterSequenceDictionary());
-    }
-
     /**
      * Add / replace the contig header lines in the VCFHeader with the in the reference file and master reference dictionary
      *
@@ -323,32 +168,20 @@ public class VCFUtils {
         return assembly;
     }
 
-    /**
-     * Read all of the VCF records from source into memory, returning the header and the VariantContexts
-     *
-     * @param source the file to read, must be in VCF4 format
-     * @return
-     * @throws IOException
-     */
-    public static Pair<VCFHeader, List<VariantContext>> readVCF(final File source) throws IOException {
-        // read in the features
-        final List<VariantContext> vcs = new ArrayList<VariantContext>();
-        final VCFCodec codec = new VCFCodec();
-        PositionalBufferedStream pbs = new PositionalBufferedStream(new FileInputStream(source));
-        FeatureCodecHeader header = codec.readHeader(pbs);
-        pbs.close();
+    /** Only displays a warning if a logger is provided and an identical warning hasn't been already issued */
+    private static final class HeaderConflictWarner {
+        Logger logger;
+        Set<String> alreadyIssued = new HashSet<String>();
 
-        pbs = new PositionalBufferedStream(new FileInputStream(source));
-        pbs.skip(header.getHeaderEnd());
-
-        final VCFHeader vcfHeader = (VCFHeader)header.getHeaderValue();
-
-        while ( ! pbs.isDone() ) {
-            final VariantContext vc = codec.decode(pbs);
-            if ( vc != null )
-                vcs.add(vc);
+        private HeaderConflictWarner(final Logger logger) {
+            this.logger = logger;
         }
 
-        return new Pair<VCFHeader, List<VariantContext>>(vcfHeader, vcs);
+        public void warn(final VCFHeaderLine line, final String msg) {
+            if ( logger != null && ! alreadyIssued.contains(line.getKey()) ) {
+                alreadyIssued.add(line.getKey());
+                logger.warn(msg);
+            }
+        }
     }
-}
\ No newline at end of file
+}
diff --git a/public/java/test/org/broadinstitute/sting/WalkerTest.java b/public/java/test/org/broadinstitute/sting/WalkerTest.java
index fa9f9e8a7..b36400a92 100755
--- a/public/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/public/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -34,12 +34,12 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.variant.bcf2.BCF2Utils;
+import org.broadinstitute.variant.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.StingException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider;
+import org.broadinstitute.variant.variantcontext.VariantContextTestProvider;
 import org.testng.Assert;
 import org.testng.annotations.AfterSuite;
 import org.testng.annotations.BeforeMethod;
diff --git a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
index be2e91557..67031a586 100755
--- a/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.commandline;
 import org.apache.commons.io.FileUtils;
 import org.broad.tribble.Feature;
 import org.broadinstitute.sting.utils.exceptions.UserException;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
diff --git a/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java b/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java
index 206f32532..307bf41a3 100644
--- a/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/commandline/RodBindingUnitTest.java
@@ -25,7 +25,7 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 import org.testng.annotations.BeforeMethod;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
index 2f73e373c..c520399e4 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/RefMetaDataTrackerUnitTest.java
@@ -36,11 +36,10 @@ import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 import org.testng.Assert;
 import org.testng.annotations.*;
 import java.util.*;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
index 48e4ff4ed..c01ed61c0 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/FeatureManagerUnitTest.java
@@ -32,11 +32,11 @@ import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.codecs.table.BedTableCodec;
 import org.broadinstitute.sting.utils.codecs.table.TableFeature;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCF3Codec;
+import org.broadinstitute.variant.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContext;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.DataProvider;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java
index 6264758ad..60a941a9e 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackBuilderUnitTest.java
@@ -29,8 +29,8 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broad.tribble.Tribble;
 import org.broad.tribble.index.Index;
-import org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCF3Codec;
+import org.broadinstitute.variant.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
index c00fbbcdb..c4e566135 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/refdata/utils/FeatureToGATKFeatureIteratorUnitTest.java
@@ -29,7 +29,7 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCFCodec;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
 import org.testng.Assert;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
index c1c22aceb..d50a8f0ae 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diffengine/DiffableReaderUnitTest.java
@@ -30,8 +30,8 @@ package org.broadinstitute.sting.gatk.walkers.diffengine;
 
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
+import org.broadinstitute.variant.vcf.VCFConstants;
+import org.broadinstitute.variant.variantcontext.Allele;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
index f7f7999be..e48c4d197 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/ArtificialReadPileupTestProvider.java
@@ -29,7 +29,7 @@ import net.sf.samtools.SAMReadGroupRecord;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.QualityUtils;
@@ -38,9 +38,6 @@ import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
 
 import java.util.*;
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
index 85528f58b..12662c748 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsUnitTest.java
@@ -1,39 +1,17 @@
 package org.broadinstitute.sting.gatk.walkers.genotyper;
 
-import net.sf.samtools.SAMFileHeader;
-import net.sf.samtools.SAMReadGroupRecord;
-import org.apache.commons.lang.ArrayUtils;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
-import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.gatk.walkers.genotyper.IndelGenotypeLikelihoodsCalculationModel;
-import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
-import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.pileup.PileupElement;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
-import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
-import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
-import org.broadinstitute.sting.utils.sam.GATKSAMReadGroupRecord;
-import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
 
 import java.util.*;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertTrue;
 
 import org.testng.Assert;
-import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 /**
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
index f6c12f443..24903bba4 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalkerUnitTest.java
@@ -37,9 +37,9 @@ import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.Variant
 import org.broadinstitute.sting.gatk.walkers.varianteval.stratifications.manager.StratificationManager;
 import org.broadinstitute.sting.gatk.walkers.varianteval.util.EvaluationContext;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 import org.testng.Assert;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.DataProvider;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
index 21d49638f..a400a004a 100644
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsUnitTest.java
@@ -2,12 +2,8 @@ package org.broadinstitute.sting.gatk.walkers.variantutils;
 
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.*;
 import org.testng.Assert;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderUnitTest;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFUtils;
 
 import org.testng.annotations.Test;
 
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
index a1d673b56..f21b662e2 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariantsIntegrationTest.java
@@ -262,7 +262,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
 
     @Test()
     public void testFileWithoutInfoLineInHeader() {
-        testFileWithoutInfoLineInHeader("testFileWithoutInfoLineInHeader", UserException.class);
+        testFileWithoutInfoLineInHeader("testFileWithoutInfoLineInHeader", IllegalStateException.class);
     }
 
     @Test()
diff --git a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
index 13db1d39e..7350e0076 100644
--- a/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/HaplotypeUnitTest.java
@@ -30,9 +30,9 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.CigarOperator;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.variantcontext.Allele;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextBuilder;
+import org.broadinstitute.variant.variantcontext.Allele;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextBuilder;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
deleted file mode 100644
index 50fbea708..000000000
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VCFJarClassLoadingUnitTest.java
+++ /dev/null
@@ -1,107 +0,0 @@
-/*
- * Copyright (c) 2011, The Broad Institute
- *
- * Permission is hereby granted, free of charge, to any person
- * obtaining a copy of this software and associated documentation
- * files (the "Software"), to deal in the Software without
- * restriction, including without limitation the rights to use,
- * copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the
- * Software is furnished to do so, subject to the following
- * conditions:
- *
- * The above copyright notice and this permission notice shall be
- * included in all copies or substantial portions of the Software.
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
- * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
- * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
- * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
- * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
- * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
- * OTHER DEALINGS IN THE SOFTWARE.
- */
-
-package org.broadinstitute.sting.utils.variantcontext;
-
-import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
-import org.testng.annotations.Test;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.net.URLClassLoader;
-
-/**
- * Test to ensure that, given only the VCF jar and its expected dependencies, core VCF classes will load.
- */
-public class VCFJarClassLoadingUnitTest {
-    @Test
-    public void testVCFJarClassLoading() throws ClassNotFoundException, MalformedURLException {
-        URL[] jarURLs;
-
-        try {
-            jarURLs = new URL[] { getVCFJarFile().toURI().toURL(), getTribbleJarFile().toURI().toURL() };
-        }
-        catch ( FileNotFoundException e ) {
-            throw new ReviewedStingException("Could not find the VCF jar and/or its dependencies", e);
-        }
-
-        ClassLoader classLoader = new URLClassLoader(jarURLs, null);
-        classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.VariantContext");
-        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec");
-        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCFCodec");
-        classLoader.loadClass("org.broadinstitute.sting.utils.codecs.vcf.VCF3Codec");
-        classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter");
-        classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.VCFWriter");
-        classLoader.loadClass("org.broadinstitute.sting.utils.variantcontext.writer.BCF2Writer");
-    }
-
-    /**
-     * Locates the tribble jar within the dist directory.
-     *
-     * Makes the horrible assumption that tests will always be run from the root of a Sting clone,
-     * but this is much less problematic than using the classpath to locate tribble, since
-     * the classpath won't explicitly contain tribble when we're testing the fully-packaged
-     * GATK jar.
-     *
-     * @return The tribble jar file, if found
-     * @throws FileNotFoundException If we couldn't locate a tribble jar within the dist directory
-     */
-    private File getTribbleJarFile() throws FileNotFoundException {
-        File distDir = new File("dist");
-        if ( ! distDir.isDirectory() ) {
-            throw new FileNotFoundException("The dist directory does not exist");
-        }
-
-        for ( File distDirEntry : distDir.listFiles() ) {
-            if ( distDirEntry.getName().startsWith("tribble") && distDirEntry.getName().endsWith(".jar") ) {
-                return distDirEntry;
-            }
-        }
-
-        throw new FileNotFoundException("Could not find a tribble jar file in the dist directory.");
-    }
-
-    /**
-     * Locates the vcf jar within the dist directory.
-     *
-     * Makes the horrible assumption that tests will always be run from the root of a Sting clone,
-     * but this is much less problematic than using the classpath to locate vcf.jar, since
-     * the classpath won't explicitly contain vcf.jar when we're testing the fully-packaged
-     * GATK jar.
-     *
-     * @return The vcf jar file, if found
-     * @throws FileNotFoundException If we couldn't locate a vcf jar within the dist directory
-     */
-    private File getVCFJarFile() throws FileNotFoundException {
-        File vcfJar = new File("dist/vcf.jar");
-
-        if ( ! vcfJar.exists() ) {
-            throw new FileNotFoundException("Could not find dist/vcf.jar");
-        }
-
-        return vcfJar;
-    }
-}
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java b/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java
similarity index 99%
rename from public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
rename to public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java
index 77050c069..5b8062b67 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2EncoderDecoderUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/bcf2/BCF2EncoderDecoderUnitTest.java
@@ -23,7 +23,7 @@
  */
 
 // our package
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
 
 // the imports for unit testing.
@@ -31,7 +31,7 @@ package org.broadinstitute.sting.utils.codecs.bcf2;
 
 import org.apache.commons.lang.ArrayUtils;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.variantcontext.writer.BCF2Encoder;
+import org.broadinstitute.variant.variantcontext.writer.BCF2Encoder;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java
rename to public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java
index ae76a374a..8a182367d 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/bcf2/BCF2UtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/bcf2/BCF2UtilsUnitTest.java
@@ -22,17 +22,14 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.bcf2;
+package org.broadinstitute.variant.bcf2;
 
-import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.vcf.*;
 
-import java.io.*;
 import java.util.*;
 import org.testng.Assert;
-import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java
rename to public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java
index 2f5aea951..8112f510d 100755
--- a/public/java/test/org/broadinstitute/sting/utils/BaseUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/utils/BaseUtilsUnitTest.java
@@ -1,5 +1,6 @@
-package org.broadinstitute.sting.utils;
+package org.broadinstitute.variant.utils;
 
+import org.broadinstitute.sting.utils.MathUtils;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java
similarity index 98%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java
index 65398c373..3ce335a00 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/AlleleUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/AlleleUnitTest.java
@@ -24,14 +24,13 @@
  */
 
 // our package
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 // the imports for unit testing.
 
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
 //    public Allele(byte[] bases, boolean isRef) {
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
index 4ce32cee7..51e600fa5 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeLikelihoodsUnitTest.java
@@ -23,13 +23,14 @@
  */
 
 // our package
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 // the imports for unit testing.
 
 
-import org.broadinstitute.sting.utils.BaseUtils;
+import org.broad.tribble.TribbleException;
+import org.broadinstitute.variant.utils.BaseUtils;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.testng.Assert;
@@ -70,7 +71,7 @@ public class GenotypeLikelihoodsUnitTest {
         Assert.assertEquals(gl.getAsString(), vPLString);
     }
 
-    @Test (expectedExceptions = UserException.MalformedVCF.class)
+    @Test (expectedExceptions = TribbleException.class)
     public void testErrorBadFormat() {
         GenotypeLikelihoods gl = GenotypeLikelihoods.fromPLField("adf,b,c");
         gl.getAsVector();
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java
index e511a7f30..7be215b2d 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypeUnitTest.java
@@ -23,7 +23,7 @@
  */
 
 // our package
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 // the imports for unit testing.
@@ -34,9 +34,6 @@ import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.Test;
 
-import java.util.Arrays;
-import java.util.List;
-
 
 public class GenotypeUnitTest extends BaseTest {
     Allele A, Aref, T;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java
similarity index 99%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java
index 6ccfd87ce..04af64bd3 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypesContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/GenotypesContextUnitTest.java
@@ -23,7 +23,7 @@
  */
 
 // our package
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 // the imports for unit testing.
@@ -33,7 +33,6 @@ import org.broad.tribble.util.ParsingUtils;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.Utils;
 import org.testng.Assert;
-import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java
similarity index 76%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java
index 0e5522e3a..bbf6976e7 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextBenchmark.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextBenchmark.java
@@ -22,21 +22,16 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import com.google.caliper.Param;
 import com.google.caliper.SimpleBenchmark;
 import com.google.caliper.runner.CaliperMain;
-import net.sf.picard.reference.ReferenceSequenceFile;
 import org.broad.tribble.Feature;
 import org.broad.tribble.FeatureCodec;
-import org.broad.tribble.readers.AsciiLineReader;
-import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.variant.vcf.VCFCodec;
 
-import java.io.*;
 import java.util.*;
 
 /**
@@ -235,7 +230,7 @@ public class VariantContextBenchmark extends SimpleBenchmark {
                             toMerge.add(new VariantContextBuilder(vc).genotypes(gc).make());
                         }
 
-                        VariantContextUtils.simpleMerge(b37GenomeLocParser, toMerge, null,
+                        VariantContextUtils.simpleMerge(toMerge, null,
                                 VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                                 VariantContextUtils.GenotypeMergeType.UNSORTED,
                                 true, false, "set", false, true);
@@ -258,54 +253,54 @@ public class VariantContextBenchmark extends SimpleBenchmark {
 
 //    public void timeV13(int rep) {
 //        for ( int i = 0; i < rep; i++ ) {
-//            FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext> func = getV13FunctionToBenchmark();
-//            FeatureCodec<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext> codec = new org.broadinstitute.sting.utils.variantcontext.v13.VCFCodec();
+//            FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext> func = getV13FunctionToBenchmark();
+//            FeatureCodec<org.broadinstitute.variant.variantcontext.v13.VariantContext> codec = new org.broadinstitute.variant.variantcontext.v13.VCFCodec();
 //            runBenchmark(codec, func);
 //        }
 //    }
 //
-//    public FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext> getV13FunctionToBenchmark() {
+//    public FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext> getV13FunctionToBenchmark() {
 //        switch ( operation ) {
 //            case READ:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        ; // empty operation
 //                    }
 //                };
 //            case SUBSET_TO_SAMPLES:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
 //                    List<String> samples;
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        if ( samples == null )
 //                            samples = new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake);
-//                        org.broadinstitute.sting.utils.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values());
+//                        org.broadinstitute.variant.variantcontext.v13.VariantContext sub = vc.subContextFromGenotypes(vc.getGenotypes(samples).values());
 //                        sub.getNSamples();
 //                    }
 //                };
 //
 //            case GET_TYPE:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getType();
 //                    }
 //                };
 //            case GET_ID:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getID();
 //                    }
 //                };
 //            case GET_GENOTYPES:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getGenotypes().size();
 //                    }
 //                };
 //
 //            case GET_GENOTYPES_FOR_SAMPLES:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
 //                    Set<String> samples;
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        if ( samples == null )
 //                            samples = new HashSet<String>(new ArrayList<String>(vc.getSampleNames()).subList(0, nSamplesToTake));
 //                        vc.getGenotypes(samples).size();
@@ -313,60 +308,60 @@ public class VariantContextBenchmark extends SimpleBenchmark {
 //                };
 //
 //            case GET_ATTRIBUTE_STRING:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getExtendedAttribute("AN", null);
 //                    }
 //                };
 //
 //            case GET_ATTRIBUTE_INT:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getAttributeAsInt("AC", 0);
 //                    }
 //                };
 //
 //            case GET_N_SAMPLES:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getNSamples();
 //                    }
 //                };
 //
 //            case GET_GENOTYPES_IN_ORDER_OF_NAME:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        ; // TODO - TEST IS BROKEN
 //                        //vc.getGenotypesOrderedByName();
 //                    }
 //                };
 //
 //            case CALC_GENOTYPE_COUNTS:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
 //                        vc.getHetCount();
 //                    }
 //                };
 //
 //            case MERGE:
-//                return new FunctionToBenchmark<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>() {
-//                    public void run(final org.broadinstitute.sting.utils.variantcontext.v13.VariantContext vc) {
-//                        List<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext> toMerge = new ArrayList<org.broadinstitute.sting.utils.variantcontext.v13.VariantContext>();
+//                return new FunctionToBenchmark<org.broadinstitute.variant.variantcontext.v13.VariantContext>() {
+//                    public void run(final org.broadinstitute.variant.variantcontext.v13.VariantContext vc) {
+//                        List<org.broadinstitute.variant.variantcontext.v13.VariantContext> toMerge = new ArrayList<org.broadinstitute.variant.variantcontext.v13.VariantContext>();
 //
 //                        for ( int i = 0; i < dupsToMerge; i++ ) {
-//                            Map<String, org.broadinstitute.sting.utils.variantcontext.v13.Genotype> gc = new HashMap<String, org.broadinstitute.sting.utils.variantcontext.v13.Genotype>();
-//                            for ( final org.broadinstitute.sting.utils.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) {
+//                            Map<String, org.broadinstitute.variant.variantcontext.v13.Genotype> gc = new HashMap<String, org.broadinstitute.variant.variantcontext.v13.Genotype>();
+//                            for ( final org.broadinstitute.variant.variantcontext.v13.Genotype g : vc.getGenotypes().values() ) {
 //                                String name = g.getSampleName()+"_"+i;
-//                                gc.put(name, new org.broadinstitute.sting.utils.variantcontext.v13.Genotype(name,
+//                                gc.put(name, new org.broadinstitute.variant.variantcontext.v13.Genotype(name,
 //                                        g.getAlleles(), g.getLog10PError(), g.getFilters(), g.getAttributes(), g.isPhased(), g.getLikelihoods().getAsVector()));
-//                                toMerge.add(org.broadinstitute.sting.utils.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc));
+//                                toMerge.add(org.broadinstitute.variant.variantcontext.v13.VariantContext.modifyGenotypes(vc, gc));
 //                            }
 //                        }
 //
-//                        org.broadinstitute.sting.utils.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser,
+//                        org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.simpleMerge(b37GenomeLocParser,
 //                                toMerge, null,
-//                                org.broadinstitute.sting.utils.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
-//                                org.broadinstitute.sting.utils.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED,
+//                                org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
+//                                org.broadinstitute.variant.variantcontext.v13.VariantContextUtils.GenotypeMergeType.UNSORTED,
 //                                true, false, "set", false, true);
 //                    }
 //                };
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java
similarity index 99%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java
index c57b2a44d..a88a76947 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextTestProvider.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextTestProvider.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import org.apache.log4j.Logger;
 import org.broad.tribble.FeatureCodec;
@@ -30,11 +30,11 @@ import org.broad.tribble.FeatureCodecHeader;
 import org.broad.tribble.readers.PositionalBufferedStream;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.*;
+import org.broadinstitute.variant.bcf2.BCF2Codec;
+import org.broadinstitute.variant.vcf.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.variantcontext.writer.Options;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.Options;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
 import org.testng.Assert;
 
 import java.io.File;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java
similarity index 96%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java
index 19620b8df..06c1bc771 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUnitTest.java
@@ -1,21 +1,19 @@
 // our package
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 
 // the imports for unit testing.
 
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.collections.Pair;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.testng.annotations.BeforeSuite;
-import org.testng.annotations.BeforeTest;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 import org.testng.Assert;
 
-import java.lang.reflect.Array;
 import java.util.*;
 
 
@@ -478,30 +476,30 @@ public class VariantContextUnitTest extends BaseTest {
         Pair<List<Integer>,byte[]> result;
         byte[] refBytes = "TATCATCATCGGA".getBytes();
 
-        Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "ATG".getBytes(), "ATGATGATGATG".getBytes()),4);
-        Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "G".getBytes(), "ATGATGATGATG".getBytes()),0);
-        Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "T".getBytes(), "T".getBytes()),1);
-        Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "AT".getBytes(), "ATGATGATCATG".getBytes()),1);
-        Assert.assertEquals(VariantContextUtils.findNumberofRepetitions( "CCC".getBytes(), "CCCCCCCC".getBytes()),2);
+        Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("ATG".getBytes(), "ATGATGATGATG".getBytes()),4);
+        Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("G".getBytes(), "ATGATGATGATG".getBytes()),0);
+        Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("T".getBytes(), "T".getBytes()),1);
+        Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("AT".getBytes(), "ATGATGATCATG".getBytes()),1);
+        Assert.assertEquals(GATKVariantContextUtils.findNumberofRepetitions("CCC".getBytes(), "CCCCCCCC".getBytes()),2);
 
-        Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("ATG".getBytes()),3);
-        Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("AAA".getBytes()),1);
-        Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("CACACAC".getBytes()),7);
-        Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("CACACA".getBytes()),2);
-        Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("CATGCATG".getBytes()),4);
-        Assert.assertEquals(VariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7);
+        Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("ATG".getBytes()),3);
+        Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AAA".getBytes()),1);
+        Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACAC".getBytes()),7);
+        Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CACACA".getBytes()),2);
+        Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("CATGCATG".getBytes()),4);
+        Assert.assertEquals(GATKVariantContextUtils.findRepeatedSubstring("AATAATA".getBytes()),7);
 
 
         // A*,ATC, context = ATC ATC ATC : (ATC)3 -> (ATC)4
         VariantContext vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStop, Arrays.asList(nullR,atc)).make();
-        result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes);
+        result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes);
         Assert.assertEquals(result.getFirst().toArray()[0],3);
         Assert.assertEquals(result.getFirst().toArray()[1],4);
         Assert.assertEquals(result.getSecond().length,3);
 
         // ATC*,A,ATCATC
         vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+3, Arrays.asList(Allele.create("AATC", true),nullA,atcatc)).make();
-        result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes);
+        result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes);
         Assert.assertEquals(result.getFirst().toArray()[0],3);
         Assert.assertEquals(result.getFirst().toArray()[1],2);
         Assert.assertEquals(result.getFirst().toArray()[2],4);
@@ -510,7 +508,7 @@ public class VariantContextUnitTest extends BaseTest {
         // simple non-tandem deletion: CCCC*, -
         refBytes = "TCCCCCCCCATG".getBytes();
         vc = new VariantContextBuilder("foo", delLoc, 10, 14, Arrays.asList(ccccR,nullA)).make();
-        result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes);
+        result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes);
         Assert.assertEquals(result.getFirst().toArray()[0],8);
         Assert.assertEquals(result.getFirst().toArray()[1],4);
         Assert.assertEquals(result.getSecond().length,1);
@@ -518,7 +516,7 @@ public class VariantContextUnitTest extends BaseTest {
         // CCCC*,CC,-,CCCCCC, context = CCC: (C)7 -> (C)5,(C)3,(C)9
         refBytes = "TCCCCCCCAGAGAGAG".getBytes();
         vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(ccccR,cc, nullA,cccccc)).make();
-        result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes);
+        result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes);
         Assert.assertEquals(result.getFirst().toArray()[0],7);
         Assert.assertEquals(result.getFirst().toArray()[1],5);
         Assert.assertEquals(result.getFirst().toArray()[2],3);
@@ -528,7 +526,7 @@ public class VariantContextUnitTest extends BaseTest {
         // GAGA*,-,GAGAGAGA
         refBytes = "TGAGAGAGAGATTT".getBytes();
         vc = new VariantContextBuilder("foo", insLoc, insLocStart, insLocStart+4, Arrays.asList(gagaR, nullA,gagagaga)).make();
-        result = VariantContextUtils.getNumTandemRepeatUnits(vc,refBytes);
+        result = GATKVariantContextUtils.getNumTandemRepeatUnits(vc, refBytes);
         Assert.assertEquals(result.getFirst().toArray()[0],5);
         Assert.assertEquals(result.getFirst().toArray()[1],3);
         Assert.assertEquals(result.getFirst().toArray()[2],7);
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUtilsUnitTest.java
similarity index 98%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUtilsUnitTest.java
index 3ad438b26..f68d24670 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantContextUtilsUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantContextUtilsUnitTest.java
@@ -21,7 +21,7 @@
  * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
  * OTHER DEALINGS IN THE SOFTWARE.
  */
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
@@ -29,6 +29,7 @@ import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
+import org.broadinstitute.sting.utils.variant.GATKVariantContextUtils;
 import org.testng.Assert;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
@@ -189,7 +190,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
         final List<String> priority = vcs2priority(inputs);
 
-        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+        final VariantContext merged = VariantContextUtils.simpleMerge(
                 inputs, priority,
                 VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.PRIORITIZE, false, false, "set", false, false);
@@ -247,7 +248,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
             inputs.add(new VariantContextBuilder(snpVC1).id(id).make());
         }
 
-        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+        final VariantContext merged = VariantContextUtils.simpleMerge(
                 inputs, null,
                 VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.UNSORTED, false, false, "set", false, false);
@@ -364,7 +365,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
     @Test(dataProvider = "mergeFiltered")
     public void testMergeFiltered(MergeFilteredTest cfg) {
         final List<String> priority = vcs2priority(cfg.inputs);
-        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+        final VariantContext merged = VariantContextUtils.simpleMerge(
                 cfg.inputs, priority, cfg.type, VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
 
         // test alleles are equal
@@ -490,7 +491,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
     @Test(dataProvider = "mergeGenotypes")
     public void testMergeGenotypes(MergeGenotypesTest cfg) {
-        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+        final VariantContext merged = VariantContextUtils.simpleMerge(
                 cfg.inputs, cfg.priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.PRIORITIZE, true, false, "set", false, false);
 
@@ -531,7 +532,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
         final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1));
         final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2));
 
-        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+        final VariantContext merged = VariantContextUtils.simpleMerge(
                 Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.UNIQUIFY, false, false, "set", false, false);
 
@@ -539,12 +540,12 @@ public class VariantContextUtilsUnitTest extends BaseTest {
         Assert.assertEquals(merged.getSampleNames(), new HashSet<String>(Arrays.asList("s1.1", "s1.2")));
     }
 
-    @Test(expectedExceptions = UserException.class)
+    @Test(expectedExceptions = IllegalStateException.class)
     public void testMergeGenotypesRequireUnique() {
         final VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), makeG("s1", Aref, T, -1));
         final VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), makeG("s1", Aref, T, -2));
 
-        final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+        final VariantContext merged = VariantContextUtils.simpleMerge(
                 Arrays.asList(vc1, vc2), null, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                 VariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE, false, false, "set", false, false);
     }
@@ -563,7 +564,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
                 VariantContext vc1 = makeVC("1", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
                 VariantContext vc2 = makeVC("2", Arrays.asList(Aref, T), VariantContext.PASSES_FILTERS);
 
-                final VariantContext merged = VariantContextUtils.simpleMerge(genomeLocParser,
+                final VariantContext merged = VariantContextUtils.simpleMerge(
                         Arrays.asList(vc1, vc2), priority, VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED,
                         VariantContextUtils.GenotypeMergeType.PRIORITIZE, annotate, false, set, false, false);
 
@@ -654,7 +655,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
     public void testRepeatDetectorTest(RepeatDetectorTest cfg) {
 
          // test alleles are equal
-        Assert.assertEquals(VariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat);
+        Assert.assertEquals(GATKVariantContextUtils.isTandemRepeat(cfg.vc, cfg.ref.getBytes()), cfg.isTrueRepeat);
     }
 
     // --------------------------------------------------------------------------------
@@ -700,7 +701,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
     @Test(dataProvider = "ReverseClippingPositionTestProvider")
     public void testReverseClippingPositionTestProvider(ReverseClippingPositionTestProvider cfg) {
-        int result = VariantContextUtils.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false);
+        int result = GATKVariantContextUtils.computeReverseClipping(cfg.alleles, cfg.ref.getBytes(), 0, false);
         Assert.assertEquals(result, cfg.expectedClip);
     }
 
@@ -778,7 +779,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
     @Test(dataProvider = "SplitBiallelics")
     public void testSplitBiallelicsNoGenotypes(final VariantContext vc, final List<VariantContext> expectedBiallelics) {
-        final List<VariantContext> biallelics = VariantContextUtils.splitVariantContextToBiallelics(vc);
+        final List<VariantContext> biallelics = GATKVariantContextUtils.splitVariantContextToBiallelics(vc);
         Assert.assertEquals(biallelics.size(), expectedBiallelics.size());
         for ( int i = 0; i < biallelics.size(); i++ ) {
             final VariantContext actual = biallelics.get(i);
@@ -799,7 +800,7 @@ public class VariantContextUtilsUnitTest extends BaseTest {
 
         final VariantContext vcWithGenotypes = new VariantContextBuilder(vc).genotypes(genotypes).make();
 
-        final List<VariantContext> biallelics = VariantContextUtils.splitVariantContextToBiallelics(vcWithGenotypes);
+        final List<VariantContext> biallelics = GATKVariantContextUtils.splitVariantContextToBiallelics(vcWithGenotypes);
         for ( int i = 0; i < biallelics.size(); i++ ) {
             final VariantContext actual = biallelics.get(i);
             Assert.assertEquals(actual.getNSamples(), vcWithGenotypes.getNSamples()); // not dropping any samples
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java
index 8f03f1d38..c29b87aad 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/VariantJEXLContextUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/VariantJEXLContextUnitTest.java
@@ -21,10 +21,9 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext;
+package org.broadinstitute.variant.variantcontext;
 
 import net.sf.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.testng.Assert;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
similarity index 95%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
index 5876efa12..048dee245 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VCFWriterUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VCFWriterUnitTest.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.AbstractFeatureReader;
@@ -31,14 +31,14 @@ import org.broad.tribble.Tribble;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderVersion;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCFHeader;
+import org.broadinstitute.variant.vcf.VCFHeaderLine;
+import org.broadinstitute.variant.vcf.VCFHeaderVersion;
 import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.*;
+import org.broadinstitute.variant.variantcontext.*;
 import org.testng.Assert;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java
similarity index 93%
rename from public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java
rename to public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java
index adf3eb235..03087051a 100644
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/writer/VariantContextWritersUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/variantcontext/writer/VariantContextWritersUnitTest.java
@@ -23,7 +23,7 @@
  */
 
 // our package
-package org.broadinstitute.sting.utils.variantcontext.writer;
+package org.broadinstitute.variant.variantcontext.writer;
 
 
 // the imports for unit testing.
@@ -33,12 +33,12 @@ import net.sf.picard.reference.IndexedFastaSequenceFile;
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broad.tribble.FeatureCodec;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.codecs.bcf2.BCF2Codec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFCodec;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
+import org.broadinstitute.variant.bcf2.BCF2Codec;
+import org.broadinstitute.variant.vcf.VCFCodec;
+import org.broadinstitute.variant.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.VariantContextTestProvider;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.VariantContextTestProvider;
 import org.testng.annotations.BeforeSuite;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java
similarity index 88%
rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
rename to public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java
index 41ea587be..b51927e0a 100755
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/IndexFactoryUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/vcf/IndexFactoryUnitTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import org.broad.tribble.AbstractFeatureReader;
@@ -9,10 +9,10 @@ import org.broad.tribble.index.IndexFactory;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.fasta.CachingIndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.variantcontext.VariantContext;
-import org.broadinstitute.sting.utils.variantcontext.writer.Options;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
+import org.broadinstitute.variant.variantcontext.VariantContext;
+import org.broadinstitute.variant.variantcontext.writer.Options;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriter;
+import org.broadinstitute.variant.variantcontext.writer.VariantContextWriterFactory;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java
similarity index 99%
rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
rename to public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java
index 62d584ef6..2ff6ebbbf 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFHeaderUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/vcf/VCFHeaderUnitTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broad.tribble.readers.AsciiLineReader;
 import org.broad.tribble.readers.PositionalBufferedStream;
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java
similarity index 97%
rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
rename to public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java
index b9ce58992..1f8e5d563 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/variant/vcf/VCFIntegrationTest.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broadinstitute.sting.WalkerTest;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -97,7 +97,7 @@ public class VCFIntegrationTest extends WalkerTest {
 
     @Test
     public void testFailingOnVCFWithoutHeaders() {
-        runVCFWithoutHeaders("", "", UserException.class, false);
+        runVCFWithoutHeaders("", "", IllegalStateException.class, false);
     }
 
     @Test
diff --git a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java b/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java
similarity index 99%
rename from public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java
rename to public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java
index b6e6c4f42..4e22603c0 100644
--- a/public/java/test/org/broadinstitute/sting/utils/codecs/vcf/VCFStandardHeaderLinesUnitTest.java
+++ b/public/java/test/org/broadinstitute/variant/vcf/VCFStandardHeaderLinesUnitTest.java
@@ -22,7 +22,7 @@
  * OTHER DEALINGS IN THE SOFTWARE.
  */
 
-package org.broadinstitute.sting.utils.codecs.vcf;
+package org.broadinstitute.variant.vcf;
 
 import org.broadinstitute.sting.BaseTest;
 import org.testng.annotations.DataProvider;
diff --git a/public/packages/GATKEngine.xml b/public/packages/GATKEngine.xml
index d0b4a52b5..27d2afa47 100644
--- a/public/packages/GATKEngine.xml
+++ b/public/packages/GATKEngine.xml
@@ -30,6 +30,8 @@
       <package name="org.broadinstitute.sting.**" />
       <!-- Tribble codecs -->
       <package name="org.broad.tribble.**" />
+      <!-- The variant package (VCF, BCF, and VariantContext) -->
+      <package name="org.broadinstitute.variant.**" />
       <!-- Workaround - depend on the logger impl required by JEXL -->
       <package name="org.apache.commons.logging.impl" />
       <!-- R packages -->
diff --git a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
index 3fe867981..b627114cf 100644
--- a/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
+++ b/public/scala/src/org/broadinstitute/sting/queue/util/VCF_BAM_utilities.scala
@@ -4,10 +4,10 @@ import java.io.File
 import org.apache.commons.io.FilenameUtils
 import scala.io.Source._
 import net.sf.samtools.SAMFileReader
-import org.broadinstitute.sting.utils.codecs.vcf.{VCFHeader, VCFCodec}
+import org.broadinstitute.variant.vcf.{VCFHeader, VCFCodec}
 import scala.collection.JavaConversions._
 import org.broad.tribble.{FeatureCodec, AbstractFeatureReader}
-import org.broadinstitute.sting.utils.variantcontext.VariantContext
+import org.broadinstitute.variant.variantcontext.VariantContext
 
 object VCF_BAM_utilities {