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 74ab7074a..43f91041f 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -607,7 +607,7 @@ public class VariantContextUtils {
         }
 
         // if we have more alternate alleles in the merged VC than in one or more of the
-        // original VCs, we need to strip out the GL/PLs (because they are no longer accurate)
+        // original VCs, we need to strip out the GL/PLs (because they are no longer accurate), as well as allele-dependent attributes like AC,AF
         for ( VariantContext vc : VCs ) {
             if (vc.alleles.size() == 1)
                 continue;
@@ -615,6 +615,8 @@ public class VariantContextUtils {
                 logger.warn(String.format("Stripping PLs at %s due incompatible alleles merged=%s vs. single=%s",
                         genomeLocParser.createGenomeLoc(vc), alleles, vc.alleles));
                 genotypes = stripPLs(genotypes);
+                // this will remove stale AC,AF attributed from vc
+                calculateChromosomeCounts(vc, attributes, true);
                 break;
             }
         }
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
index e30187a7c..5a4d6e6a1 100755
--- a/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariantsIntegrationTest.java
@@ -96,8 +96,8 @@ public class CombineVariantsIntegrationTest extends WalkerTest {
 
     @Test public void uniqueSNPs() { combine2("pilot2.snps.vcf4.genotypes.vcf", "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf", "", "78a49597f1abf1c738e67d50c8fbed2b"); }
 
-    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "9253d61ddb52c429adf0e153cef494ca"); }
-    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "5012dfe65cf7e7d8f014e97e4a996aea"); }
+    @Test public void omniHM3Union() { combineSites(" -filteredRecordsMergeType KEEP_IF_ANY_UNFILTERED", "4c63bfa5f73793aaca42e130ec49f238"); }
+    @Test public void omniHM3Intersect() { combineSites(" -filteredRecordsMergeType KEEP_IF_ALL_UNFILTERED", "86e326acbd8d2af8a6040eb146d92fc6"); }
 
     @Test public void threeWayWithRefs() {
         WalkerTestSpec spec = new WalkerTestSpec(