From 481630da00d2060290defb6e7d0ca6fb9a93cb40 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 9 Aug 2011 11:10:29 -0400 Subject: [PATCH] BWA parameters added --- .../sting/queue/qscripts/RecalibrateBaseQualities.scala | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala index 75e8c8325..9f3dd9a2c 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala @@ -110,7 +110,7 @@ class RecalibrateBaseQualities extends QScript { case class align(@Input inFastq: File, @Output outSam: File) extends ExternalCommonArgs { - def commandLine = bwaPath + " bwasw " + reference + " " + inFastq + " > " + outSam + def commandLine = bwaPath + " bwasw -b5 -q2 -r1 -z10 -t8 " + reference + " " + inFastq + " > " + outSam this.analysisName = queueLogDir + outSam + ".bwa_sam_se" this.jobName = queueLogDir + outSam + ".bwa_sam_se" }