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updates to MDCP 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5586 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-04-06 19:44:46 +00:00
parent 3f3f35dea0
commit febb883511
1 changed files with 5 additions and 5 deletions
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10
scala/qscript/core/MethodsDevelopmentCallingPipeline.scala
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@ -115,7 +115,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
"HiSeq19" -> new Target("NA12878.HiSeq19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 97.0, !lowPass),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 98.0, !lowPass),
"GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
@ -248,11 +248,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile, "known=false,training=true,truth=true,prior=12.0")
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile, "known=false,training=true,truth=true,prior=15.0")
if( t.hapmapFile.contains("b37") )
this.rodBind :+= RodBind("omni", "VCF", omni_b37, "known=false,training=true,truth=true,prior=15.0")
this.rodBind :+= RodBind("omni", "VCF", omni_b37, "known=false,training=true,truth=false,prior=12.0")
else if( t.hapmapFile.contains("b36") )
this.rodBind :+= RodBind("omni", "VCF", omni_b36, "known=false,training=true,truth=true,prior=15.0")
this.rodBind :+= RodBind("omni", "VCF", omni_b36, "known=false,training=true,truth=false,prior=12.0")
if (t.dbsnpFile.endsWith(".rod"))
this.rodBind :+= RodBind("dbsnp", "DBSNP", t.dbsnpFile, "known=true,training=false,truth=false,prior=10.0")
else if (t.dbsnpFile.endsWith(".vcf"))
@ -260,7 +260,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile }
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.allPoly = true
this.fixOmni = true // temporary argument until new Omni file is released
this.tranche ++= List("100.0", "99.9", "99.5", "99.3", "99.0", "98.9", "98.8", "98.5", "98.4", "98.3", "98.2", "98.1", "98.0", "97.9", "97.8", "97.5", "97.0", "95.0", "90.0")
this.analysisName = t.name + "_VQSR"
this.jobName = queueLogDir + t.name + ".VQSR"