diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
index c629bd313..aca9e21af 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/AllelePair.java
@@ -35,6 +35,10 @@ public class AllelePair {
     private Allele bottom;
 
     public AllelePair(Genotype gt) {
+        if ( gt.isNoCall() ) {
+            // do nothing
+            return;
+        }
         if (gt.getPloidy() != 2)
             throw new ReviewedStingException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString());