minor dataset chages.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5289 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro
parent
318035c147
commit
8ea71fd294
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@ -1,5 +1,3 @@
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import org.broadinstitute.sting.commandline.ArgumentSource
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import org.broadinstitute.sting.gatk.CommandLineGATK
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import org.broadinstitute.sting.queue.extensions.gatk._
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.gatk.phonehome.GATKRunReport
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@ -75,7 +73,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")
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val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta")
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val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
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val dbSNP_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_hg18.rod"
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val dbSNP_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_hg18.rod" // Special case for NA12878 collections that can't use 132 because they are part of it.
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val dbSNP_hg18_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_hg18.rod"
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val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_130_b36.rod"
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val dbSNP_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_132_b37.leftAligned.vcf"
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val dbSNP_b37_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.rod" // Special case for NA12878 collections that can't use 132 because they are part of it.
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@ -107,15 +106,19 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"),
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new File("/humgen/gsa-scr1/carneiro/prj/hiseq19/analysis/snps/NA12878.hg19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass), // ** we need a chunked hg19 whole genome intervals file **
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"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
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new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
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new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
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"WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18, hapmap_hg18,
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"WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18_129, hapmap_hg18,
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"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask",
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new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"),
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new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"),
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"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 2.6, !lowPass),
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"WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
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new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
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new File("/humgen/gsa-scr1/carneiro/prj/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
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"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass),
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"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
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new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
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new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
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"TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
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new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people
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new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
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@ -131,12 +134,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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"LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
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new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
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new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
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"WExTrio" -> new Target("CEUTrio.WEx", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
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new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
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new File("/humgen/gsa-scr1/carneiro/prj/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
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"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass)
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass)
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)
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@ -154,16 +152,16 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val goldStandard = true
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for (target <- targets) {
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if( !skipCalling ) {
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add(new UnifiedGenotyper(target))
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add(new VariantFiltration(target))
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add(new GenerateVariantClusters(target, !goldStandard))
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add(new Call(target))
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add(new Filter(target))
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add(new GenerateClusters(target, !goldStandard))
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add(new VariantRecalibratorTiTv(target, !goldStandard))
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add(new VariantRecalibratorNRS(target, !goldStandard))
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if (!noCut) add (new VariantCut(target))
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if (eval) add(new VariantEvaluation(target))
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}
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if ( !skipGoldStandard ) {
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add(new GenerateVariantClusters(target, goldStandard))
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add(new GenerateClusters(target, goldStandard))
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add(new VariantRecalibratorTiTv(target, goldStandard))
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add(new VariantRecalibratorNRS(target, goldStandard))
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}
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@ -175,7 +173,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val FiltersToIgnore = List("DPFilter", "ABFilter", "ESPStandard", "QualByDepth", "StrandBias", "HomopolymerRun")
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// 1.) Call SNPs with UG
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class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
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class Call (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
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this.reference_sequence = t.reference
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this.intervalsString ++= List(t.intervals)
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this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20
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@ -188,7 +186,9 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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this.analysisName = t.name + "_UG"
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if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile)
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else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
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/*
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//todo -- beautify scattergather directory structure
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/*
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this.setupScatterFunction = {
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case scatter: ScatterFunction =>
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scatter.commandDirectory = new File("UG/ScatterGather")
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@ -204,11 +204,11 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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gather.commandDirectory = new File("UG/ScatterGather/Gather_%s".format(source.field.getName))
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gather.jobOutputFile = new File(".queue/UG/ScatterGather/Gather_%s.out".format(source.field.getName))
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}
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*/
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*/
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}
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// 2.) Filter SNPs
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class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration with UNIVERSAL_GATK_ARGS {
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class Filter (t: Target) extends VariantFiltration with UNIVERSAL_GATK_ARGS {
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this.reference_sequence = t.reference
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this.intervalsString ++= List(t.intervals)
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this.scatterCount = 10
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@ -224,7 +224,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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}
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// 3.) VQSR part1 Generate Gaussian clusters based on truth sites
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class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS {
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class GenerateClusters(t: Target, goldStandard: Boolean) extends GenerateVariantClusters with UNIVERSAL_GATK_ARGS {
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val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
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this.reference_sequence = t.reference
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this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
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@ -246,7 +246,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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}
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// 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters
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class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS {
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class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
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val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
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this.reference_sequence = t.reference
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if( t.hapmapFile.contains("b37") )
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@ -284,8 +284,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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this.tranchesFile = t.tsTranchesFile
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}
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// 5.) Variant Cut (OPTIONAL!) filter out the variants marked by recalibration to the 99% tranche
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class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
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// 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche
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class VariantCut(t: Target) extends ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
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this.reference_sequence = t.reference
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this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
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this.analysisName = t.name + "_VC"
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@ -299,8 +299,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
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}
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// 6.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
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class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS {
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// 6.) Variant Evaluation (OPTIONAL) based on the sensitivity recalibrated vcf
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class VariantEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
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val name: String = t.name
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this.reference_sequence = t.reference
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this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
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