diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
index 4f115b46e..ec67563dc 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/beagle/BeagleOutputToVCFWalker.java
@@ -320,8 +320,7 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
             og = a1+"/"+a2;
 
             // See if Beagle switched genotypes
-            if (!((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) ||
-                    (bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA))))){
+            if (! originalAlleleA.equals(Allele.NO_CALL) && beagleSwitchedGenotypes(bglAlleleA,originalAlleleA,bglAlleleB,originalAlleleB)){
                 originalAttributes.put("OG",og);
                 numGenotypesChangedByBeagle++;
             }
@@ -364,6 +363,11 @@ public class BeagleOutputToVCFWalker  extends RodWalker<Integer, Integer> {
         return 1;
     }
 
+    private boolean beagleSwitchedGenotypes(Allele bglAlleleA, Allele originalAlleleA, Allele bglAlleleB, Allele originalAlleleB) {
+       return !((bglAlleleA.equals(originalAlleleA) && bglAlleleB.equals(originalAlleleB) ||
+                    (bglAlleleA.equals(originalAlleleB) && bglAlleleB.equals(originalAlleleA))));
+    }
+
     public Integer reduceInit() {
         return 0; // Nothing to do here
     }