diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
index 09936c112..4aa580052 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotype.java
@@ -64,7 +64,6 @@ public enum DiploidGenotype {
             return r != base2;
         else
             return base2 == r;
-        //return MathUtils.countOccurrences(r, this.toString()) == 1;
     }
 
     public boolean isHom() {
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
index 20b1b0b14..23d4e4905 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SNPGenotypeLikelihoodsCalculationModel.java
@@ -176,7 +176,7 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
             final double[] likelihoods = sampleData.GL.getLikelihoods();
             final int PLindexOfBestGL = MathUtils.maxElementIndex(likelihoods);
             if ( PLindexOfBestGL != PLindexOfRef ) {
-                GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePair(3, PLindexOfBestGL);
+                GenotypeLikelihoods.GenotypeLikelihoodsAllelePair alleles = GenotypeLikelihoods.getAllelePairUsingDeprecatedOrdering(PLindexOfBestGL);
                 if ( alleles.alleleIndex1 != baseIndexOfRef )
                     likelihoodSums[alleles.alleleIndex1] += likelihoods[PLindexOfBestGL] - likelihoods[PLindexOfRef];
                 // don't double-count it
diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
index 54b4cf230..cc0d9788b 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -272,6 +272,29 @@ public class GenotypeLikelihoods {
         return PLIndexToAlleleIndex[PLindex];
     }
 
+    // An index conversion from the deprecated PL ordering to the new VCF-based ordering for up to 3 alternate alleles
+    protected static int[] PLindexConversion = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9};
+
+    /**
+     * get the allele index pair for the given PL using the deprecated PL ordering:
+     *    AA,AB,AC,AD,BB,BC,BD,CC,CD,DD instead of AA,AB,BB,AC,BC,CC,AD,BD,CD,DD.
+     * Although it's painful to keep this conversion around, our DiploidSNPGenotypeLikelihoods class uses the deprecated
+     *    ordering and I know with certainty that external users have built code on top of it; changing it now would
+     *    cause a whole lot of heartache for our collaborators, so for now at least there's a standard conversion method.
+     * This method assumes at most 3 alternate alleles.
+     * TODO -- address this issue at the source by updating DiploidSNPGenotypeLikelihoods.
+     *
+     * @param PLindex   the PL index
+     * @return the allele index pair
+     */
+    public static GenotypeLikelihoodsAllelePair getAllelePairUsingDeprecatedOrdering(final int PLindex) {
+        // make sure that we've cached enough data
+        if ( PLindex >= PLIndexToAlleleIndex.length )
+            calculatePLcache(PLindex);
+
+        return PLIndexToAlleleIndex[PLindexConversion[PLindex]];
+    }
+
     /**
      * get the PL indexes (AA, AB, BB) for the given allele pair; assumes allele1Index <= allele2Index.
      *
diff --git a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java b/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
index 6320a140d..638fd2531 100755
--- a/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
+++ b/public/java/test/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoodsUnitTest.java
@@ -137,13 +137,10 @@ public class GenotypeLikelihoodsUnitTest {
 
     @Test
     public void testCalculatePLindex(){
-        // AA,AB,BB,AC,BC,CC,AD,BD,CD,DD called in the order of AA,AB,AC,AD,BB,BC,BD,CC,CD,DD
-        int[] indexes = new int[]{0, 1, 3, 6, 2, 4, 7, 5, 8, 9};
-
         int counter = 0;
         for ( int i = 0; i <= 3; i++ ) {
             for ( int j = i; j <= 3; j++ ) {
-                Assert.assertEquals(GenotypeLikelihoods.calculatePLindex(i, j), indexes[counter++], "PL index of alleles " + i + "," + j + " was not calculated correctly");
+                Assert.assertEquals(GenotypeLikelihoods.calculatePLindex(i, j), GenotypeLikelihoods.PLindexConversion[counter++], "PL index of alleles " + i + "," + j + " was not calculated correctly");
             }
         }
     }