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 47c93bb1b..8c8e4f257 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/GenotypeLikelihoods.java
@@ -101,9 +101,12 @@ public class GenotypeLikelihoods {
     }
 
     //Return genotype likelihoods as an EnumMap with Genotypes as keys and likelihoods as values
+    //Returns null in case of missing likelihoods
     public EnumMap<Genotype.Type,Double> getAsMap(boolean normalizeFromLog10){
         //Make sure that the log10likelihoods are set
         double[] likelihoods = normalizeFromLog10 ? MathUtils.normalizeFromLog10(getAsVector()) : getAsVector();
+        if(likelihoods == null)
+            return null;
         EnumMap<Genotype.Type,Double> likelihoodsMap = new EnumMap<Genotype.Type, Double>(Genotype.Type.class);
         likelihoodsMap.put(Genotype.Type.HOM_REF,likelihoods[Genotype.Type.HOM_REF.ordinal()-1]);
         likelihoodsMap.put(Genotype.Type.HET,likelihoods[Genotype.Type.HET.ordinal()-1]);
@@ -112,10 +115,13 @@ public class GenotypeLikelihoods {
     }
 
     //Return the neg log10 Genotype Quality (GQ) for the given genotype
+    //Returns Double.NEGATIVE_INFINITY in case of missing genotype
     public double getNegLog10GQ(Genotype.Type genotype){
 
         double qual = Double.NEGATIVE_INFINITY;
         EnumMap<Genotype.Type,Double> likelihoods = getAsMap(false);
+        if(likelihoods == null)
+            return qual;
         for(Map.Entry<Genotype.Type,Double> likelihood : likelihoods.entrySet()){
             if(likelihood.getKey() == genotype)
                 continue;