From a4defdfb292e623d34543d38b8b58fdc267f2426 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 12 Jun 2012 09:39:17 -0400
Subject: [PATCH] Adding a GT header line to SomaticIndelDetector output

---
 .../sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java    | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
index 9705b265c..806a9c2a5 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/SomaticIndelDetectorWalker.java
@@ -316,6 +316,7 @@ public class SomaticIndelDetectorWalker extends ReadWalker<Integer,Integer> {
         // first, the basic info
         headerInfo.add(new VCFHeaderLine("source", "SomaticIndelDetector"));
         headerInfo.add(new VCFHeaderLine("reference", getToolkit().getArguments().referenceFile.getName()));
+        headerInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
 
         // FORMAT and INFO fields
 //        headerInfo.addAll(VCFUtils.getSupportedHeaderStrings());