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 aca9e21af..c629bd313 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
@@ -35,10 +35,6 @@ 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());
 
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
index 07cd95997..f4369401b 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/GenotypePhasingEvaluator.java
@@ -119,7 +119,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
             if (evalSampGenotypes != null)
                 evalSampGt = evalSampGenotypes.get(samp);
 
-            if (compSampGt == null || evalSampGt == null) { // Since either comp or eval (or both) are missing the site, the best we can do is hope to preserve phase [if the non-missing one preserves phase]
+            if (compSampGt == null || evalSampGt == null || compSampGt.isNoCall() || evalSampGt.isNoCall()) { // Since either comp or eval (or both) are missing the site, the best we can do is hope to preserve phase [if the non-missing one preserves phase]
                 // Having an unphased site breaks the phasing for the sample [does NOT permit "transitive phasing"] - hence, must reset phasing knowledge for both comp and eval [put a null CompEvalGenotypes]:
                 if (isNonNullButUnphased(compSampGt) || isNonNullButUnphased(evalSampGt))
                     samplePrevGenotypes.put(samp, null);
@@ -209,7 +209,7 @@ public class GenotypePhasingEvaluator extends VariantEvaluator {
     }
 
     public boolean isNonNullButUnphased(Genotype gt) {
-        return (gt != null && !genotypesArePhasedAboveThreshold(gt));
+        return (gt != null && !gt.isNoCall() && !genotypesArePhasedAboveThreshold(gt));
     }
 
     public boolean genotypesArePhasedAboveThreshold(Genotype gt) {