diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
index 418c2f483..550ba9624 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Allele.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Allele.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
 import org.broadinstitute.sting.utils.BaseUtils;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Genotype.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Genotype.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Genotype.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Genotype.java
index df1667456..327d9767d 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/Genotype.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/Genotype.java
@@ -1,7 +1,6 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
 
@@ -12,6 +11,7 @@ import java.util.*;
  */
 public class Genotype {
     protected InferredGeneticContext commonInfo;
+    public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
     protected List<Allele> alleles = new ArrayList<Allele>();
 
     public Genotype(String sampleName, List<Allele> alleles, double negLog10PError, Set<String> filters, Map<String, ?> attributes) {
@@ -25,7 +25,7 @@ public class Genotype {
     }
 
     public Genotype(String sampleName, List<Allele> alleles) {
-        this(sampleName, alleles, InferredGeneticContext.NO_NEG_LOG_10PERROR, null, null);
+        this(sampleName, alleles, NO_NEG_LOG_10PERROR, null, null);
     }
 
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/InferredGeneticContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/InferredGeneticContext.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/InferredGeneticContext.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/InferredGeneticContext.java
index 085c2d016..402fabacf 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/InferredGeneticContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/InferredGeneticContext.java
@@ -1,6 +1,5 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
-import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableGenotype.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableGenotype.java
similarity index 96%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableGenotype.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableGenotype.java
index dc08504db..252c40566 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableGenotype.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableGenotype.java
@@ -1,6 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
-
-import org.broadinstitute.sting.utils.Utils;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableVariantContext.java
similarity index 98%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableVariantContext.java
index 72c08e862..de62c9916 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/MutableVariantContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/MutableVariantContext.java
@@ -1,8 +1,7 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.BaseUtils;
 
 import java.util.*;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java
index 0ffc5ef9b..0a868f316 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContext.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.StingException;
@@ -160,6 +160,7 @@ import java.util.*;
  */
 public class VariantContext {
     protected InferredGeneticContext commonInfo = null;
+    public final static double NO_NEG_LOG_10PERROR = InferredGeneticContext.NO_NEG_LOG_10PERROR;
 
     /** The location of this VariantContext */
     private GenomeLoc loc;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
similarity index 99%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java
rename to java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index b2ec1a6f7..9e8520a27 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -1,11 +1,10 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.contexts.variantcontext;
 
 import java.util.*;
 import org.apache.commons.jexl.*;
 import org.broadinstitute.sting.utils.StingException;
 import org.broadinstitute.sting.utils.Utils;
 
-
 public class VariantContextUtils {
     /** 
      * A simple but common wrapper for matching VariantContext objects using JEXL expressions
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
similarity index 95%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java
rename to java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
index 6c10d7b5f..381eff78a 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextAdaptors.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/VariantContextAdaptors.java
@@ -1,10 +1,11 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.gatk.refdata.rodDbSNP;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeRecord;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFGenotypeEncoding;
 import org.broadinstitute.sting.utils.genotype.vcf.VCFRecord;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
 
 import java.util.*;
 
@@ -143,7 +144,7 @@ public class VariantContextAdaptors {
                 for ( VCFGenotypeEncoding s : vcfG.getAlleles() )
                     genotypeAlleles.add(Allele.getMatchingAllele(alleles, s.getBases()));
 
-                double pError = vcfG.getNegLog10PError() == VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY ? InferredGeneticContext.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();
+                double pError = vcfG.getNegLog10PError() == VCFGenotypeRecord.MISSING_GENOTYPE_QUALITY ? Genotype.NO_NEG_LOG_10PERROR : vcfG.getNegLog10PError();
 
                 Map<String, String> fields = new HashMap<String, String>();
                 for ( Map.Entry<String, String> e : vcfG.getFields().entrySet() ) {
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
similarity index 97%
rename from java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java
rename to java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
index 81022549e..87b792fd3 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/variantcontext/TestVariantContextWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestVariantContextWalker.java
@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.oneoffprojects.variantcontext;
+package org.broadinstitute.sting.oneoffprojects.walkers;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
index 2c6afaa04..df2fb9201 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/CountVariants.java
@@ -3,8 +3,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java
index 867972f71..2abcba93a 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/DbSNPPercentage.java
@@ -3,12 +3,8 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.*;
-import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.StingException;
-import org.broadinstitute.sting.utils.genotype.Variation;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
 
 import java.util.ArrayList;
 import java.util.List;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
index f43059d13..5b705845e 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/MendelianViolationEvaluator.java
@@ -3,14 +3,13 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.Allele;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Genotype;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.Allele;
 import org.broadinstitute.sting.utils.StingException;
 
 import java.util.List;
 import java.util.Arrays;
-import java.util.ArrayList;
 import java.util.regex.Pattern;
 import java.util.regex.Matcher;
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java
index a53d1d87b..032a18550 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/TiTvVariantEvaluator.java
@@ -3,9 +3,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.StingException;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.Arrays;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
index fb8f6ef3c..e8d4b8ada 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEval2Walker.java
@@ -2,14 +2,13 @@ package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextAdaptors;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextUtils;
 import org.apache.log4j.Logger;
 
 import java.util.*;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java
index 289aab923..99d0e46e0 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/varianteval2/VariantEvaluator.java
@@ -1,9 +1,9 @@
 package org.broadinstitute.sting.oneoffprojects.walkers.varianteval2;
 
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 
 import java.util.List;
 import java.util.ArrayList;
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
index 8045f1c8a..b4321027c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/diagnostics/SNPDensity.java
@@ -1,19 +1,13 @@
 package org.broadinstitute.sting.playground.gatk.walkers.diagnostics;
 
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
-import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
-import org.broadinstitute.sting.gatk.refdata.RODRecordList;
-import org.broadinstitute.sting.gatk.refdata.RodVCF;
+import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.cmdLine.Argument;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.Pair;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContext;
-import org.broadinstitute.sting.oneoffprojects.variantcontext.VariantContextAdaptors;
-
-import java.util.*;
 
 /**
  * Computes the density of SNPs passing and failing filters in intervals on the genome and emits a table for display
diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/variantcontext/AlleleTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/variantcontext/AlleleTest.java
similarity index 100%
rename from java/test/org/broadinstitute/sting/oneoffprojects/variantcontext/AlleleTest.java
rename to java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/variantcontext/AlleleTest.java
diff --git a/java/test/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextTest.java b/java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/variantcontext/VariantContextTest.java
similarity index 100%
rename from java/test/org/broadinstitute/sting/oneoffprojects/variantcontext/VariantContextTest.java
rename to java/test/org/broadinstitute/sting/gatk/contexts/variantcontext/variantcontext/VariantContextTest.java