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Added the R script for VQSR 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5898 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro 2011-05-27 21:56:56 +00:00
parent 77cae39c8e
commit 2524216d4b
1 changed files with 4 additions and 1 deletions
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5
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -74,6 +74,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val filteredIndelVCF = new File(name + ".filtered.indel.vcf")
val recalibratedVCF = new File(name + ".recalibrated.vcf")
val tranchesFile = new File(name + ".tranches")
val vqsrRscript = name + ".vqsr.r"
val recalFile = new File(name + ".tranches.recal")
val goldStandardRecalibratedVCF = new File(name + "goldStandard.recalibrated.vcf")
val goldStandardTranchesFile = new File(name + "goldStandard.tranches")
@ -217,6 +218,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.baq = if (noBAQ) {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"
this.A ++= List("FisherStrand")
}
// 1b.) Call Indels with UG
@ -262,11 +264,12 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.rodBind :+= RodBind("dbsnp", "DBSNP", t.dbsnpFile, "known=true,training=false,truth=false,prior=10.0")
else if (t.dbsnpFile.endsWith(".vcf"))
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile, "known=true,training=false,truth=false,prior=10.0")
this.use_annotation ++= List("QD", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "HRun")
this.use_annotation ++= List("QD", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "HRun", "FS")
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile }
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.allPoly = true
this.tranche ++= List("100.0", "99.9", "99.5", "99.3", "99.0", "98.9", "98.8", "98.5", "98.4", "98.3", "98.2", "98.1", "98.0", "97.9", "97.8", "97.5", "97.0", "95.0", "90.0")
this.rscript_file = t.vqsrRscript
this.analysisName = t.name + "_VQSR"
this.jobName = queueLogDir + t.name + ".VQSR"
}