diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
index fd9d388e5..595ac5fe5 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DindelGenotypeLikelihoodsCalculationModel.java
@@ -33,8 +33,6 @@ import org.broadinstitute.sting.gatk.walkers.indels.HaplotypeIndelErrorModel;
 import org.broadinstitute.sting.gatk.walkers.indels.PairHMMIndelErrorModel;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.GenomeLoc;
-import org.broadinstitute.sting.utils.GenomeLocParser;
-import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
index d9f6a3420..271792200 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCalcLikelihoods.java
@@ -111,11 +111,11 @@ public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer>
     }
 
     public Integer reduce(VariantCallContext value, Integer sum) {
-        if ( value == null || value.vc == null )
+        if ( value == null )
             return sum;
 
         try {
-            writer.add(value.vc, value.refBase);
+            writer.add(value, value.refBase);
         } catch (IllegalArgumentException e) {
             throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
         }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
index aae84fbba..4a6ab0eaf 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UGCallVariants.java
@@ -110,13 +110,13 @@ public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
     public Integer reduceInit() { return 0; }
 
     public Integer reduce(VariantCallContext value, Integer sum) {
-        if ( value == null || value.vc == null )
+        if ( value == null )
             return sum;
 
         try {
-            Map<String, Object> attrs = new HashMap<String, Object>(value.vc.getAttributes());
-            VariantContextUtils.calculateChromosomeCounts(value.vc, attrs, true);
-            writer.add(VariantContext.modifyAttributes(value.vc, attrs), value.refBase);
+            Map<String, Object> attrs = new HashMap<String, Object>(value.getAttributes());
+            VariantContextUtils.calculateChromosomeCounts(value, attrs, true);
+            writer.add(VariantContext.modifyAttributes(value, attrs), value.refBase);
         } catch (IllegalArgumentException e) {
             throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
         }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
index b2ea35249..085708571 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
@@ -561,14 +561,14 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
         Allele alt = null;
         for ( Map.Entry<String,StratifiedAlignmentContext> sEntry : strat.entrySet() ) {
             VariantCallContext call = engine.calculateLikelihoodsAndGenotypes(tracker, ref, sEntry.getValue().getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE));
-            if ( call != null && call.confidentlyCalled && call.vc != null ) {
-                if ( call.vc.isSNP() ) {
-                    if ( ! call.vc.getAlternateAllele(0).basesMatch(var.getAlternateAllele(0))) {
+            if ( call != null && call.confidentlyCalled ) {
+                if ( call.isSNP() ) {
+                    if ( ! call.getAlternateAllele(0).basesMatch(var.getAlternateAllele(0))) {
                         if ( alt == null ) {
-                            alt = call.vc.getAlternateAllele(0);
-                            conf = (int) Math.floor(10*call.vc.getNegLog10PError());
+                            alt = call.getAlternateAllele(0);
+                            conf = (int) Math.floor(10*call.getNegLog10PError());
                         } else {
-                            conf += (int) Math.floor(10*call.vc.getNegLog10PError());
+                            conf += (int) Math.floor(10*call.getNegLog10PError());
                         }
                     }
                 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
index 71d8bd1ed..1a2025d0d 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
@@ -199,10 +199,10 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
 
     private Genotype getGenotype( RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context ) {
         VariantCallContext calls = ug.calculateLikelihoodsAndGenotypes(tracker,ref,context);
-        if ( calls == null || calls.vc == null || calls.vc.getNSamples() == 0 || !calls.vc.isSNP() )
+        if ( calls == null || calls.getNSamples() == 0 || !calls.isSNP() )
             return null;
         else {
-            return calls.vc.getGenotype(0);
+            return calls.getGenotype(0);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
index 58d2c4646..12a5f372c 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/SnpCallRateByCoverageWalker.java
@@ -120,8 +120,8 @@ public class SnpCallRateByCoverageWalker extends LocusWalker<List<String>, Strin
 
                         VariantCallContext calls = UG.calculateLikelihoodsAndGenotypes(tracker, ref, subContext);
 
-                        if (calls != null && calls.vc != null && calls.vc.getNSamples() > 0 && calls.confidentlyCalled) {
-                            Genotype evCall = calls.vc.getGenotype(0);
+                        if (calls != null && calls.getNSamples() > 0 && calls.confidentlyCalled) {
+                            Genotype evCall = calls.getGenotype(0);
                             vcCall = vc.getGenotype(evCall.getSampleName());
 
                             if ((evCall.isHet() || evCall.isHomVar()) && (vcCall.isHet() || vcCall.isHomVar())) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java
index 37a522dc1..08a74a431 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ValidationGenotyper.java
@@ -178,7 +178,7 @@ public class ValidationGenotyper extends LocusWalker<ValidationGenotyper.Counted
         }
         else if( evalStatus == VARIANT_STATUS.CALLED && compStatus == VARIANT_STATUS.MISSING ) {
             VariantCallContext call = engine.calculateLikelihoodsAndGenotypes(tracker, ref, context);
-            if( call != null && call.confidentlyCalled && call.vc != null && call.vc.getType() == VariantContext.Type.NO_VARIATION ) {
+            if( call != null && call.confidentlyCalled && call.getType() == VariantContext.Type.NO_VARIATION ) {
                 counter.numFP = 1L;
                 if( printStream!= null ) {
                     printStream.println(vcEval.getChr() + ":" + vcEval.getStart() ); // Used to create interval lists of FP variants
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
index 8d344109a..5bcfdd80f 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/contamination/FindContaminatingReadGroupsWalker.java
@@ -109,8 +109,8 @@ public class FindContaminatingReadGroupsWalker extends LocusWalker<Integer, Inte
         if (altBalance > 0.70) {
             VariantCallContext ugResult = ug.calculateLikelihoodsAndGenotypes(tracker, ref, context);
 
-            if (ugResult != null && ugResult.vc != null && ugResult.vc.getNSamples() > 0) {
-                return ugResult.vc.getGenotype(0).isHet();
+            if (ugResult != null && ugResult.getNSamples() > 0) {
+                return ugResult.getGenotype(0).isHet();
             }
         }