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 574ef6ab8..42e1b471f 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
@@ -1601,7 +1601,8 @@ public class GATKVariantContextUtils {
      * @param indexesOfRelevantAlleles the indexes of the original alleles corresponding to the new alleles
      * @return non-null array of new AD values
      */
-    private static int[] generateAD(final int[] originalAD, final int[] indexesOfRelevantAlleles) {
+    protected static int[] generateAD(final int[] originalAD, final int[] indexesOfRelevantAlleles) {
+        if ( originalAD == null || indexesOfRelevantAlleles == null ) throw new IllegalArgumentException("The list of input AD values and alleles must not be null");
 
         final int numADs = indexesOfRelevantAlleles.length;
         if ( numADs == originalAD.length )
@@ -1610,11 +1611,11 @@ public class GATKVariantContextUtils {
         final int[] newAD = new int[numADs];
 
         for ( int i = 0; i < numADs; i++ ) {
-            final int newIndex = indexesOfRelevantAlleles[i];
-            if ( newIndex >= originalAD.length )
+            final int oldIndex = indexesOfRelevantAlleles[i];
+            if ( oldIndex >= originalAD.length )
                 newAD[i] = 0;
             else
-                newAD[newIndex] = originalAD[i];
+                newAD[i] = originalAD[oldIndex];
         }
 
         return newAD;
diff --git a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
index bc198198f..0f6c0855a 100644
--- a/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
+++ b/public/gatk-framework/src/test/java/org/broadinstitute/sting/utils/variant/GATKVariantContextUtilsUnitTest.java
@@ -1662,14 +1662,14 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
         }
 
         for (final Allele other : otherAlleles) {
-            Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,true,true,true),-1);
+            Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc, other, true, true, true), -1);
             Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,false,true,true),-1);
             Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,true,true,false),-1);
             Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,false,true,false),-1);
             Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,true,false,true),-1);
             Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,false,false,true),-1);
             Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,true,false,false),-1);
-            Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc,other,false,false,false),-1);
+            Assert.assertEquals(GATKVariantContextUtils.indexOfAllele(vc, other, false, false, false),-1);
         }
     }
 
@@ -1708,5 +1708,15 @@ public class GATKVariantContextUtilsUnitTest extends BaseTest {
             }
         };
     }
+
+    @Test
+    public void testGenerateADWithNewAlleles() {
+
+        final int[] originalAD = new int[] {1,2,0};
+        final int[] indexesOfRelevantAlleles = new int[] {0,1,2,2};
+        
+        final int[] newAD = GATKVariantContextUtils.generateAD(originalAD, indexesOfRelevantAlleles);
+        Assert.assertEquals(newAD, new int[]{1,2,0,0});
+    }
 }