diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
index 10c5293a6..942d81bf4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -203,6 +203,9 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
             return 0;
 
         VariantContext vc = tracker.getVariantContext(ref, "variant", null, context.getLocation(), true);
+	if ( vc == null ){
+	    return 0;
+	}
         VariantContext sub = subsetRecord(vc, samples);
 
         if ( (sub.isPolymorphic() || !EXCLUDE_NON_VARIANTS) && (!sub.isFiltered() || !EXCLUDE_FILTERED) ) {