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 11c9c3a99..0104f24d9 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
@@ -6,6 +6,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatible;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.ExperimentalAnnotation;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
+import org.broadinstitute.sting.gatk.walkers.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
@@ -24,7 +25,14 @@ import java.util.List;
  */
 public class AlleleBalanceBySample extends GenotypeAnnotation implements ExperimentalAnnotation {
 
-    public void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext stratifiedContext, VariantContext vc, Genotype g, final GenotypeBuilder gb) {
+    public void annotate(final RefMetaDataTracker tracker,
+                         final AnnotatorCompatible walker,
+                         final ReferenceContext ref,
+                         final AlignmentContext stratifiedContext,
+                         final VariantContext vc,
+                         final Genotype g,
+                         final GenotypeBuilder gb,
+                         final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
         Double ratio = annotateSNP(stratifiedContext, vc, g);
         if (ratio == null)
             return;
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 cd8faf093..8922bf54a 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
@@ -6,6 +6,7 @@ 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.gatk.walkers.annotator.interfaces.StandardAnnotation;
+import org.broadinstitute.sting.gatk.walkers.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;
@@ -48,7 +49,8 @@ public class DepthPerAlleleBySample extends GenotypeAnnotation implements Standa
                          final AlignmentContext stratifiedContext,
                          final VariantContext vc,
                          final Genotype g,
-                         final GenotypeBuilder gb) {
+                         final GenotypeBuilder gb,
+                         final PerReadAlleleLikelihoodMap alleleLikelihoodMap) {
         if ( g == null || !g.isCalled() )
             return;
 
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 b5252f15b..354b798bb 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
@@ -30,6 +30,7 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 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.gatk.walkers.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;
@@ -46,14 +47,19 @@ import java.util.List;
  * Count for each sample of mapping quality zero reads
  */
 public class MappingQualityZeroBySample extends GenotypeAnnotation {
-    public void annotate(RefMetaDataTracker tracker,
-                         AnnotatorCompatible walker, ReferenceContext ref, AlignmentContext context,
-                         VariantContext vc, Genotype g, GenotypeBuilder gb) {
+    public void annotate(final RefMetaDataTracker tracker,
+                         final AnnotatorCompatible walker,
+                         final ReferenceContext ref,
+                         final AlignmentContext stratifiedContext,
+                         final VariantContext vc,
+                         final Genotype g,
+                         final GenotypeBuilder gb,
+                         final PerReadAlleleLikelihoodMap alleleLikelihoodMap){
         if ( g == null || !g.isCalled() )
             return;
 
         int mq0 = 0;
-        final ReadBackedPileup pileup = context.getBasePileup();
+        final ReadBackedPileup pileup = stratifiedContext.getBasePileup();
         for (PileupElement p : pileup ) {
             if ( p.getMappingQual() == 0 )
                 mq0++;
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 f30fb4109..fd7968747 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
@@ -210,7 +210,7 @@ public class VariantAnnotatorEngine {
         VariantContextBuilder builder = new VariantContextBuilder(vc).attributes(infoAnnotations);
 
         // annotate genotypes, creating another new VC in the process
-        return builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc)).make();
+        return builder.genotypes(annotateGenotypes(tracker, ref, stratifiedContexts, vc, perReadAlleleLikelihoodMap)).make();
     }
 
     public VariantContext annotateContext(final Map<String, PerReadAlleleLikelihoodMap> stratifiedContexts, VariantContext vc) {
@@ -278,20 +278,25 @@ public class VariantAnnotatorEngine {
         }
     }
 
-    private GenotypesContext annotateGenotypes(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
+    private GenotypesContext annotateGenotypes(final RefMetaDataTracker tracker,
+                                               final ReferenceContext ref, final Map<String, AlignmentContext> stratifiedContexts,
+                                               final VariantContext vc,
+                                               final Map<String,PerReadAlleleLikelihoodMap> stratifiedPerReadAlleleLikelihoodMap) {
         if ( requestedGenotypeAnnotations.isEmpty() )
             return vc.getGenotypes();
 
         final GenotypesContext genotypes = GenotypesContext.create(vc.getNSamples());
         for ( final Genotype genotype : vc.getGenotypes() ) {
-            AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
+            final AlignmentContext context = stratifiedContexts.get(genotype.getSampleName());
+            final PerReadAlleleLikelihoodMap perReadAlleleLikelihoodMap = stratifiedPerReadAlleleLikelihoodMap.get(genotype.getSampleName());
 
-            if ( context == null ) {
+            if ( context == null && perReadAlleleLikelihoodMap == null) {
+                // no likelihoods nor pileup available: just move on to next sample
                 genotypes.add(genotype);
             } else {
                 final GenotypeBuilder gb = new GenotypeBuilder(genotype);
                 for ( final GenotypeAnnotation annotation : requestedGenotypeAnnotations ) {
-                    annotation.annotate(tracker, walker, ref, context, vc, genotype, gb);
+                    annotation.annotate(tracker, walker, ref, context, vc, genotype, gb, perReadAlleleLikelihoodMap);
                 }
                 genotypes.add(gb.make());
             }
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 bc20f6c97..6c55c1c00 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
@@ -3,6 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.annotator.interfaces;
 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.genotyper.PerReadAlleleLikelihoodMap;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
 import org.broadinstitute.sting.utils.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.variantcontext.GenotypeBuilder;
@@ -13,9 +14,14 @@ import java.util.List;
 public abstract class GenotypeAnnotation extends VariantAnnotatorAnnotation {
 
     // return annotations for the given contexts/genotype split by sample
-    public abstract void annotate(RefMetaDataTracker tracker, AnnotatorCompatible walker,
-                                  ReferenceContext ref, AlignmentContext stratifiedContext,
-                                  VariantContext vc, Genotype g, GenotypeBuilder gb );
+    public abstract void annotate(final RefMetaDataTracker tracker,
+                                  final AnnotatorCompatible walker,
+                                  final ReferenceContext ref,
+                                  final AlignmentContext stratifiedContext,
+                                  final VariantContext vc,
+                                  final Genotype g,
+                                  final GenotypeBuilder gb,
+                                  final PerReadAlleleLikelihoodMap alleleLikelihoodMap);
 
     // return the descriptions used for the VCF FORMAT meta field
     public abstract List<VCFFormatHeaderLine> getDescriptions();