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BWA parameters added

This commit is contained in:
Mauricio Carneiro 2011-08-09 11:10:29 -04:00
parent 22d2563823
commit 481630da00
1 changed files with 1 additions and 1 deletions
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public/scala/qscript/org/broadinstitute/sting/queue/qscripts/RecalibrateBaseQualities.scala
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@ -110,7 +110,7 @@ class RecalibrateBaseQualities extends QScript {
case class align(@Input inFastq: File, @Output outSam: File) extends ExternalCommonArgs { 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.analysisName = queueLogDir + outSam + ".bwa_sam_se"
this.jobName = queueLogDir + outSam + ".bwa_sam_se" this.jobName = queueLogDir + outSam + ".bwa_sam_se"
} }