From 6d7ed5781cd0c6709650c3268af509dcc9d442cc Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 26 Oct 2010 22:22:28 +0000
Subject: [PATCH] Added Dbsnp to Indel Realigner; added known indels
 rod-binding to realigner.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4576 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/fullCallingPipeline.q | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 6f98e0547..d5b291808 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -124,6 +124,8 @@ class fullCallingPipeline extends QScript {
         realigner.intervals = Nil
         realigner.intervalsString = Nil
         realigner.scatterCount = num_cleaner_scatter_jobs min contigs.size
+        realigner.DBSNP = qscript.pipeline.getProject.getDbsnpFile
+        realigner.rodbind :+= RodBind("indels", "VCF", swapExt(qscript.pipeline.getProject.getReferenceFile, "fasta", "1kg_pilot_indels.vcf") 
 
         // if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates
         if (realigner.scatterCount > 1) {