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adding dbsnp to indel VQSR

This commit is contained in:
Mauricio Carneiro 2012-01-10 12:38:35 -05:00
parent e923a2e512
commit 5bf960deb8
1 changed files with 3 additions and 2 deletions
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5
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -299,8 +299,9 @@ class MethodsDevelopmentCallingPipeline extends QScript {
}
class indelRecal(t: Target) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS {
this.input :+= t.rawIndelVCF
this.resource :+= new TaggedFile( indelGoldStandardCallset, "known=true,training=true,truth=true,prior=12.0" )
this.input :+= t.rawIndelVCF
this.resource :+= new TaggedFile(indelGoldStandardCallset, "known=false,training=true,truth=true,prior=12.0" )
this.resource :+= new TaggedFile( t.dbsnpFile, "known=true,prior=2.0" )
this.use_annotation ++= List("QD", "HaplotypeScore", "ReadPosRankSum", "FS")
if(t.nSamples >= 10)
this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate