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Misc cleanup in Methods Development Qscript 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4878 348d0f76-0448-11de-a6fe-93d51630548a
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rpoplin 2010-12-20 04:24:25 +00:00
parent 34ab5b4889
commit 8fac346ac1
1 changed files with 10 additions and 28 deletions
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38
scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala
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@ -90,12 +90,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod") this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.scatterCount = 64 this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
if( t.isLowpass ) { this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } )
this.dcov = Some(50)
} else {
this.dcov = Some(250)
}
this.input_file :+= t.bamList this.input_file :+= t.bamList
this.out = t.rawVCF this.out = t.rawVCF
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE) this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.RECALCULATE)
@ -118,44 +114,30 @@ class MethodsDevelopmentCallingPipeline extends QScript {
// 3.) VQSR part1 Generate Gaussian clusters based on truth sites // 3.) VQSR part1 Generate Gaussian clusters based on truth sites
class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS { class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS {
var name: String = t.name val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
if( goldStandard ) { name = t.goldStandardName }
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod") this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf") this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
if( goldStandard ) { this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
this.rodBind :+= RodBind("input", "VCF", t.goldStandard_VCF) this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
this.clusterFile = t.goldStandardClusterFile
} else {
this.rodBind :+= RodBind("input", "VCF", t.filteredVCF)
this.clusterFile = t.clusterFile
}
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
this.analysisName = name + "_GVC" this.analysisName = name + "_GVC"
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.qual = Some(300) this.qual = Some(300) // clustering parameters to be updated soon pending new experimentation results
this.std = Some(3.5) this.std = Some(3.5)
this.mG = Some(16) // v2 calls this.mG = Some(16)
// ignores
this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= FiltersToIgnore
} }
// 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters // 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters
class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS { class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS {
var name: String = t.name val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
if( goldStandard ) { name = t.goldStandardName }
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod") this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod")
this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf") this.rodBind :+= RodBind("hapmap", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
this.rodBind :+= RodBind("truth", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf") this.rodBind :+= RodBind("truth", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr." + t.rodName + "_fwd.vcf")
if( goldStandard ) { this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
this.rodBind :+= RodBind("input", "VCF", t.goldStandard_VCF) this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
this.clusterFile = t.goldStandardClusterFile
} else {
this.rodBind :+= RodBind("input", "VCF", t.filteredVCF)
this.clusterFile = t.clusterFile
}
this.analysisName = name + "_VR" this.analysisName = name + "_VR"
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= FiltersToIgnore