diff --git a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
index 5787b591f..da80a3431 100755
--- a/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
+++ b/public/java/src/org/broadinstitute/sting/utils/variantcontext/VariantContext.java
@@ -867,7 +867,10 @@ public class VariantContext implements Feature { // to enable tribble intergrati
 
         for ( String name : sampleNames ) {
             if ( map.containsKey(name) ) throw new IllegalArgumentException("Duplicate names detected in requested samples " + sampleNames);
-            map.put(name, getGenotype(name));
+            final Genotype g = getGenotype(name);
+            if ( g != null ) {
+                map.put(name, g);
+            }
         }
 
         return map;