diff --git a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
index 4af465c69..1c169decc 100644
--- a/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
+++ b/protected/gatk-protected/src/test/java/org/broadinstitute/sting/gatk/walkers/variantutils/GenotypeGVCFsIntegrationTest.java
@@ -65,7 +65,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("0d056d8f09dfaf9e34eec28747bb6f33"));
+                Arrays.asList("09575e44c9dbcd171a30eff43961c57f"));
         executeTest("combineSingleSamplePipelineGVCF", spec);
     }
 
@@ -90,7 +90,7 @@ public class GenotypeGVCFsIntegrationTest extends WalkerTest {
                         " -V:sample3 " + privateTestDir + "combine.single.sample.pipeline.3.vcf" +
                         " -L 20:10,000,000-20,000,000", b37KGReference),
                 1,
-                Arrays.asList("3552f61d15375afb753879cb0bcd2880"));
+                Arrays.asList("3f34e05318479cf8743f4227491c7cd1"));
         executeTest("combineSingleSamplePipelineGVCFHierarchical", spec);
     }
 
diff --git a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
index 57f7b4175..892cabf61 100644
--- a/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
+++ b/public/gatk-framework/src/main/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtils.java
@@ -582,7 +582,7 @@ public class GATKVariantContextUtils {
     }
 
     /**
-     * Create the new GenotypesContext with the subsetted PLs
+     * Create the new GenotypesContext with the subsetted PLs and ADs
      *
      * @param originalGs               the original GenotypesContext
      * @param vc                       the original VariantContext
@@ -643,7 +643,7 @@ public class GATKVariantContextUtils {
             newGTs.add(gb.make());
         }
 
-        return newGTs;
+        return fixADFromSubsettedAlleles(newGTs, vc, allelesToUse);
     }
 
     private static boolean likelihoodsAreUninformative(final double[] likelihoods) {
@@ -1087,10 +1087,10 @@ public class GATKVariantContextUtils {
         if ( refAllele == null )
             return null;
 
-        // FinalAlleleSet contains the alleles of the new resulting VC.
-        // Using linked set in order to guaranteed an stable order:
+        // FinalAlleleSet contains the alleles of the new resulting VC
+        // Using linked set in order to guarantee a stable order
         final LinkedHashSet<Allele> finalAlleleSet = new LinkedHashSet<>(10);
-        // Reference goes first:
+        // Reference goes first
         finalAlleleSet.add(refAllele);
 
         final Map<String, Object> attributes = new LinkedHashMap<>();
@@ -1321,20 +1321,18 @@ public class GATKVariantContextUtils {
         if ( numNewAlleles == numOriginalAlleles )
             return oldGs;
 
-        final GenotypesContext newGs = fixPLsFromSubsettedAlleles(oldGs, originalVC, selectedVC.getAlleles());
-
-        return fixADFromSubsettedAlleles(newGs, originalVC, selectedVC.getAlleles());
+        return fixGenotypesFromSubsettedAlleles(oldGs, originalVC, selectedVC.getAlleles());
     }
 
     /**
-     * Fix the PLs for the GenotypesContext of a VariantContext that has been subset
+     * Fix the PLs and ADs for the GenotypesContext of a VariantContext that has been subset
      *
      * @param originalGs       the original GenotypesContext
      * @param originalVC       the original VariantContext
      * @param allelesToUse     the new (sub)set of alleles to use
      * @return a new non-null GenotypesContext
      */
-    static private GenotypesContext fixPLsFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List<Allele> allelesToUse) {
+    static private GenotypesContext fixGenotypesFromSubsettedAlleles(final GenotypesContext originalGs, final VariantContext originalVC, final List<Allele> allelesToUse) {
 
         // we need to determine which of the alternate alleles (and hence the likelihoods) to use and carry forward
         final List<Integer> likelihoodIndexesToUse = determineLikelihoodIndexesToUse(originalVC, allelesToUse);