From 5bf960deb81d0c4d350c8d2d89280067e157d922 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Tue, 10 Jan 2012 12:38:35 -0500 Subject: [PATCH] adding dbsnp to indel VQSR --- .../queue/qscripts/MethodsDevelopmentCallingPipeline.scala | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala index b50bf3d67..2f0715ae9 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -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