From 623c49765d7a70cd87e68cee913bd133eaf168aa Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Thu, 22 Sep 2011 11:13:40 -0400
Subject: [PATCH] NO BAQ ON EXOMES!

says the boss.
---
 .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala      | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
index 29ee2769b..34bc43ff5 100755
--- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
+++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
@@ -221,7 +221,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
       this.max_deletion_fraction = qscript.deletions
     this.out = t.rawVCF
     this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
-    this.baq = if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
+    this.baq = if (noBAQ ||  t.isExome) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
     this.analysisName = t.name + "_UGs"
     this.jobName =  queueLogDir + t.name + ".snpcall"
   }