diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
index 007ad966d..d0d0cd6ef 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/QualByDepth.java
@@ -66,6 +66,8 @@ public class QualByDepth implements InfoFieldAnnotation, StandardAnnotation {
     public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Float, "Variant Confidence/Quality by Depth")); }
 
     private double getQual(double[] GLs) {
+        if ( GLs == null )
+            return 0.0;        
 
         // normalize so that we don't have precision issues
         double[] adjustedLikelihoods = new double[GLs.length];