From eccb76c304c0699c352d69fa27ec8e586151d989 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Tue, 30 Oct 2012 15:09:46 -0400
Subject: [PATCH] Only run UG in the bundle for chr20

---
 .../sting/queue/qscripts/GATKResourcesBundle.scala               | 1 +
 1 file changed, 1 insertion(+)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
index 951e380c3..24ab50451 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
@@ -317,6 +317,7 @@ class GATKResourcesBundle extends QScript {
   class UG(@Input bam: File, @Input ref: File, @Input outVCF: File) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
     this.input_file = List(bam)
     this.reference_sequence = ref
+    this.intervalsString ++= List("20");
     this.out = outVCF
   }