From 0f4ace0902830b7fc8527333b01dc95f7c877224 Mon Sep 17 00:00:00 2001
From: carneiro <carneiro@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 29 Mar 2011 18:24:19 +0000
Subject: [PATCH] fixed a bug when the concordance track doesn't have the
 sample in the variant track.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5535 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 5be627a89..ccf5ac29a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/SelectVariants.java
@@ -164,7 +164,7 @@ 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;
                         }