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Updating the MDCP with the new indel gold standard from Ryan.

This commit is contained in:
Mauricio Carneiro 2012-01-09 15:31:18 -05:00
parent f01f7d1db8
commit 6f2abd76df
1 changed files with 3 additions and 3 deletions
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6
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -92,7 +92,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val training_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.highQuality.vcf" val training_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.highQuality.vcf"
val badSites_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.terrible.vcf" val badSites_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.terrible.vcf"
val projectConsensus_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/ALL.wgs.projectConsensus_v2b.20101123.snps.sites.vcf" val projectConsensus_1000G = "/humgen/1kg/processing/official_release/phase1/projectConsensus/ALL.wgs.projectConsensus_v2b.20101123.snps.sites.vcf"
val millsDevine_b37 = "/humgen/gsa-hpprojects/GATK/bundle/current/b37/Mills_Devine_2hit.indels.b37.sites.vcf" val indelGoldStandardCallset = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf"
val lowPass: Boolean = true val lowPass: Boolean = true
val exome: Boolean = true val exome: Boolean = true
@ -300,7 +300,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
class indelRecal(t: Target) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS { class indelRecal(t: Target) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS {
this.input :+= t.rawIndelVCF this.input :+= t.rawIndelVCF
this.resource :+= new TaggedFile( millsDevine_b37, "known=true,training=true,truth=true,prior=12.0" ) this.resource :+= new TaggedFile( indelGoldStandardCallset, "known=true,training=true,truth=true,prior=12.0" )
this.use_annotation ++= List("QD", "HaplotypeScore", "ReadPosRankSum", "FS") this.use_annotation ++= List("QD", "HaplotypeScore", "ReadPosRankSum", "FS")
if(t.nSamples >= 10) if(t.nSamples >= 10)
this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate
@ -365,7 +365,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 5b.) Indel Evaluation (OPTIONAL) // 5b.) Indel Evaluation (OPTIONAL)
class indelEvaluation(t: Target) extends EvalBase(t) { class indelEvaluation(t: Target) extends EvalBase(t) {
this.eval :+= t.recalibratedIndelVCF this.eval :+= t.recalibratedIndelVCF
this.comp :+= new TaggedFile(millsDevine_b37, "mills" ) this.comp :+= new TaggedFile(indelGoldStandardCallset, "indelGS" )
this.noEV = true this.noEV = true
this.evalModule = List("CompOverlap", "CountVariants", "TiTvVariantEvaluator", "ValidationReport", "IndelStatistics") this.evalModule = List("CompOverlap", "CountVariants", "TiTvVariantEvaluator", "ValidationReport", "IndelStatistics")
this.out = t.evalIndelFile this.out = t.evalIndelFile