From 5e0c4ecc2133fdd9d2943dccd08eab75234c4683 Mon Sep 17 00:00:00 2001
From: corin <corin@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 14 Oct 2010 17:02:17 +0000
Subject: [PATCH] Added DbSnp to VariantEval

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4497 348d0f76-0448-11de-a6fe-93d51630548a
---
 scala/qscript/fullCallingPipeline.q | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 1ac789f9f..416a5d57a 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -1,7 +1,7 @@
 import net.sf.picard.reference.FastaSequenceFile
 import org.broadinstitute.sting.datasources.pipeline.Pipeline
-import org.broadinstitute.sting.gatk.DownsampleType
 import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeCalculationModel.Model
+import org.broadinstitute.sting.gatk.{CommandLineGATK, DownsampleType}
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.extensions.picard.PicardBamJarFunction
 import org.broadinstitute.sting.queue.extensions.samtools._
@@ -313,6 +313,7 @@ class fullCallingPipeline extends QScript {
     eval.reportLocation = new File(base+".eval")
     eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
     eval.analysisName = base+"_VariantEval"
+    eval.DBSNP = qscript.pipeline.getProject.getDBSNP
 
     add(snps)