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 6905ce4a4..3fed4542c 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
@@ -31,6 +31,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContextUtils;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.baq.BAQ;
 import org.broadinstitute.sting.utils.exceptions.StingException;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
@@ -122,6 +123,11 @@ public class SNPGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsC
             aList.add(refAllele);
             aList.add(altAllele);
             double[] dlike = new double[]{likelihoods[refGenotype.ordinal()],likelihoods[hetGenotype.ordinal()],likelihoods[homGenotype.ordinal()]} ;
+            double maxElement = MathUtils.max(dlike[AlleleFrequencyCalculationModel.GenotypeType.AA.ordinal()],
+                    dlike[AlleleFrequencyCalculationModel.GenotypeType.AB.ordinal()],dlike[AlleleFrequencyCalculationModel.GenotypeType.BB.ordinal()]);
+            for (int i=0; i < dlike.length; i++)
+                 dlike[i] -= maxElement;
+
             GLs.put(sample.getKey(), new MultiallelicGenotypeLikelihoods(sample.getKey(),
                     aList,  dlike, getFilteredDepth(pileup)));
         }
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
index 3e3b29a7f..40b704570 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/CombineVariants.java
@@ -274,11 +274,11 @@ public class CombineVariants extends RodWalker<Integer, Integer> {
         else {
             mergedVCs = preMergedVCs;
         }
-
         for ( VariantContext mergedVC : mergedVCs ) {
             // only operate at the start of events
             if ( mergedVC == null )
                 continue;
+            System.out.println(mergedVC.toString());
 
             HashMap<String, Object> attributes = new HashMap<String, Object>(mergedVC.getAttributes());
             // re-compute chromosome counts
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 ca9c71eba..806bd2013 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContextUtils.java
@@ -594,7 +594,9 @@ 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)
         for ( VariantContext vc : VCs ) {
-            if ( vc.alleles.size() != alleles.size() ) {
+            if (vc.alleles.size() == 1)
+                continue;
+            if ( vc.alleles.size() != alleles.size()) {
                 genotypes = stripPLs(genotypes);
                 break;
             }