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Use Context not Dinuc covariate

This commit is contained in:
Eric Banks 2012-07-17 15:18:11 -04:00
parent b0d99fd10d
commit 863eb5b5c0
2 changed files with 2 additions and 2 deletions
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2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala
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@ -345,7 +345,7 @@ class DataProcessingPipeline extends QScript {
case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs { case class cov (inBam: File, outRecalFile: File) extends BaseQualityScoreRecalibrator with CommandLineGATKArgs {
this.knownSites ++= qscript.dbSNP this.knownSites ++= qscript.dbSNP
this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= Seq("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.out = outRecalFile this.out = outRecalFile
if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform if (!defaultPlatform.isEmpty) this.default_platform = defaultPlatform

2
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala
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@ -164,7 +164,7 @@ class PacbioProcessingPipeline extends QScript {
if (resetQuals) if (resetQuals)
this.DBQ = dbq this.DBQ = dbq
this.knownSites :+= dbSNP this.knownSites :+= dbSNP
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate") this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "ContextCovariate")
this.input_file :+= inBam this.input_file :+= inBam
this.out = outRecalFile this.out = outRecalFile
this.analysisName = queueLogDir + outRecalFile + ".covariates" this.analysisName = queueLogDir + outRecalFile + ".covariates"