From 5d0f284305ec4274ec255474a1cd536574fc1a39 Mon Sep 17 00:00:00 2001 From: Ryan Poplin Date: Wed, 21 Sep 2011 20:26:28 -0400 Subject: [PATCH] Fixing exome specific arguments to the VQSR in the methods development calling pipeline --- .../qscripts/MethodsDevelopmentCallingPipeline.scala | 9 +++++++-- 1 file changed, 7 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 29ee2769b..d187c1e1a 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala @@ -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 }