From 06b1497902d3c2e5e6036a5772eeb1e584398f65 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Wed, 13 Apr 2011 15:02:09 +0000
Subject: [PATCH] Corrected bad merge.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5625 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../sting/gatk/walkers/variantutils/SelectVariants.java         | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

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;
                         }