From db2e2cb0ff9fbccadd83d218f2064c18fde95a88 Mon Sep 17 00:00:00 2001
From: delangel <delangel@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 25 Jan 2011 19:05:31 +0000
Subject: [PATCH] Another trivial change to make VQSR work with indels

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5073 348d0f76-0448-11de-a6fe-93d51630548a
---
 .../gatk/walkers/variantrecalibration/ApplyVariantCuts.java   | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
index 877013f87..5d3802439 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyVariantCuts.java
@@ -142,8 +142,8 @@ public class ApplyVariantCuts extends RodWalker<Integer, Integer> {
             return 1;
         }
 
-        for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) {
-            if( vc != null && vc.isSNP() ) {
+        for( VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), true, false) ) {
+            if( vc != null ) {
                 String filterString = null;
                 if( !vc.isFiltered() ) {
                     try {