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 c3e06100a..15c17988c 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
@@ -701,9 +701,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
 
         GenotypesContext newGC = sub.getGenotypes();
 
-        // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs (because they are no longer accurate)
+        // if we have fewer alternate alleles in the selected VC than in the original VC, we need to strip out the GL/PLs and AD (because they are no longer accurate)
         if ( vc.getAlleles().size() != sub.getAlleles().size() )
-            newGC = VariantContextUtils.stripPLs(sub.getGenotypes());
+            newGC = VariantContextUtils.stripPLsAndAD(sub.getGenotypes());
 
         // if we have fewer samples in the selected VC than in the original VC, we need to strip out the MLE tags
         if ( vc.getNSamples() != sub.getNSamples() ) {
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
index bd8d86d73..6ae81f76f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -157,11 +157,8 @@ public class VariantContextUtils {
         builder.attributes(calculateChromosomeCounts(vc, new HashMap<String, Object>(vc.getAttributes()), removeStaleValues, founderIds));
     }
 
-    public static Genotype removePLs(Genotype g) {
-        if ( g.hasLikelihoods() )
-            return new GenotypeBuilder(g).noPL().make();
-        else
-            return g;
+    public static Genotype removePLsAndAD(final Genotype g) {
+        return ( g.hasLikelihoods() || g.hasAD() ) ? new GenotypeBuilder(g).noPL().noAD().make() : g;
     }
 
     public final static VCFCompoundHeaderLine getMetaDataForField(final VCFHeader header, final String field) {
@@ -581,7 +578,7 @@ public class VariantContextUtils {
                 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));
-                genotypes = stripPLs(genotypes);
+                genotypes = stripPLsAndAD(genotypes);
                 // this will remove stale AC,AF attributed from vc
                 calculateChromosomeCounts(vc, attributes, true);
                 break;
@@ -672,11 +669,11 @@ public class VariantContextUtils {
         return true;
     }
 
-    public static GenotypesContext stripPLs(GenotypesContext genotypes) {
+    public static GenotypesContext stripPLsAndAD(GenotypesContext genotypes) {
         GenotypesContext newGs = GenotypesContext.create(genotypes.size());
 
         for ( final Genotype g : genotypes ) {
-            newGs.add(g.hasLikelihoods() ? removePLs(g) : g);
+            newGs.add(removePLsAndAD(g));
         }
 
         return newGs;
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 ffd9c9b4a..34395e920 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
@@ -255,7 +255,7 @@ public class SelectVariantsIntegrationTest extends WalkerTest {
         WalkerTestSpec spec = new WalkerTestSpec(
                 "-T SelectVariants -R " + b37KGReference + " -o %s --no_cmdline_in_header -sf " + samplesFile + " --excludeNonVariants --variant " + testfile,
                 1,
-                Arrays.asList("3ab35d5e81a29fb5db3e2add11c7e823")
+                Arrays.asList("f14d75892b99547d8e9ba3a03bfb04ea")
         );
         executeTest("test select from multi allelic with excludeNonVariants --" + testfile, spec);
     }