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 e0415ce82..574a13792 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -217,7 +217,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> {
                     // if the genotype of any of the samples we're looking it is HET or HomVar, we write this variant
                     for (String sample : samples) {
                         Genotype g = compVC.getGenotype(sample);
-                        if ( g.isHet() || g.isHomVar() ) {
+                        if ( g != null && (g.isHet() || g.isHomVar()) ) {
                             vcfWriter.add(compVC, ref.getBase());
                             return 1;
                         }