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Fixing exome specific arguments to the VQSR in the methods development calling pipeline

This commit is contained in:
Ryan Poplin 2011-09-21 20:26:28 -04:00
parent 74f9ccf6dd
commit 5d0f284305
1 changed files with 7 additions and 2 deletions
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9
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -266,13 +266,18 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.resource :+= new TaggedFile( t.dbsnpFile, "known=true,prior=2.0" )
this.resource :+= new TaggedFile( projectConsensus_1000G, "prior=8.0" )
this.use_annotation ++= List("QD", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "MQ", "FS")
if(t.nSamples >= 10) {
if(t.nSamples >= 10) { // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate
this.use_annotation ++= List("InbreedingCoeff")
}
if(!t.isExome) {
this.use_annotation ++= List("DP")
} else {
} else { // exome specific parameters
this.resource :+= new TaggedFile( badSites_1000G, "bad=true,prior=2.0" )
this.mG = 6
if(t.nSamples <= 3) { // very few exome samples means very few variants
this.mG = 4
this.percentBad = 0.04
}
}
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile }
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }