dpp: back to using 4gb memory assuming all is right with IndelRealigner now.
mdcp: Some class structural changes due to the inclusion of indel calls. ApplyCut now chooses the tranche differently for each dataset. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5319 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
carneiro
parent
3e0a722672
commit
81414a21dd
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@ -1,7 +1,17 @@
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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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import org.broadinstitute.sting.queue.function.scattergather.{GatherFunction, CloneFunction, ScatterFunction}
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// ToDos:
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// reduce the scope of the datasets so the script is more nimble
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// figure out how to give names to all the Queue-LSF logs (other than Q-1931@node1434-24.out) so that it is easier to find logs for certain steps
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// create gold standard BAQ'd bam files, no reason to always do it on the fly
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// Analysis to add at the end of the script:
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// auto generation of the cluster plots
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// spike in NA12878 to the exomes and to the lowpass, analysis of how much of her variants are being recovered compared to single sample exome or HiSeq calls
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// produce Kiran's Venn plots based on comparison between new VCF and gold standard produced VCF
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class MethodsDevelopmentCallingPipeline extends QScript {
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@ -57,6 +67,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val goldStandard_VCF: File,
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val intervals: String,
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val titvTarget: Double,
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val trancheTarget: Double,
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val isLowpass: Boolean) {
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val name = qscript.outputDir + baseName
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val clusterFile = new File(name + ".clusters")
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@ -69,7 +80,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val tsRecalibratedVCF = new File(name + ".ts.recalibrated.vcf")
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val tsTranchesFile = new File(name + ".ts.tranches")
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val cutVCF = new File(name + ".cut.vcf")
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val evalFile = new File(name + ".eval")
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val evalFile = new File(name + ".snp.eval")
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val evalIndelFile = new File(name + ".indel.eval")
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val goldStandardName = qscript.outputDir + "goldStandard/" + baseName
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val goldStandardClusterFile = new File(goldStandardName + ".clusters")
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}
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@ -81,69 +93,64 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val dbSNP_hg18_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_hg18.rod" // Special case for NA12878 collections that can't use 132 because they are part of it.
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val dbSNP_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_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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val dbSNP_b37_129 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/dbSNP/dbsnp_129_b37.leftAligned.vcf" // Special case for NA12878 collections that can't use 132 because they are part of it.
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val hapmap_hg18 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.hg18_fwd.vcf"
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val hapmap_b36 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b36_fwd.vcf"
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val hapmap_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"
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val omni_b37 = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/1212samples.b37.vcf"
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val indelMask_b36 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b36.bed"
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val indelMask_b37 = "/humgen/1kg/processing/pipeline_test_bams/pilot1.dindel.mask.b37.bed"
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// ToDos:
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// reduce the scope of the datasets so the script is more nimble
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// figure out how to give names to all the Queue-LSF logs (other than Q-1931@node1434-24.out) so that it is easier to find logs for certain steps
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// create gold standard BAQ'd bam files, no reason to always do it on the fly
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// Analysis to add at the end of the script:
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// auto generation of the cluster plots
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// spike in NA12878 to the exomes and to the lowpass, analysis of how much of her variants are being recovered compared to single sample exome or HiSeq calls
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// produce Kiran's Venn plots based on comparison between new VCF and gold standard produced VCF
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val lowPass: Boolean = true
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val indels: Boolean = true
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val useMask: Boolean = !noMASK
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val useCut: Boolean = !noCut
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val queueLogDir = ".qlog/"
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val targetDataSets: Map[String, Target] = Map(
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"HiSeq" -> new Target("NA12878.HiSeq", hg18, dbSNP_hg18_129, hapmap_hg18,
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"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
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new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
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new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, 1.0, !lowPass),
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"HiSeq19" -> new Target("NA12878.HiSeq19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
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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-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 1.0, !lowPass),
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"GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37_129, hapmap_b37, indelMask_b37,
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new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"),
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new File("/humgen/gsa-hpprojects/dev/carneiro/hiseq19/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, !lowPass),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 1.0, !lowPass),
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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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"/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, 3.0, !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-hpprojects/dev/carneiro/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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"/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, 3.0, !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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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 1.0, 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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"/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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"/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, 1.0, !lowPass),
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"LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36,
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new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from
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new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), // the gold standard VCF file to run through the VQSR
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, lowPass), // chunked interval list to use with Queue's scatter/gather functionality
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, 1.0, lowPass), // chunked interval list to use with Queue's scatter/gather functionality
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"LowPassAugust" -> new Target("ALL.august.v4", b37, dbSNP_b37, hapmap_b37, indelMask_b37, // BUGBUG: kill this, it is too large
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new File("/humgen/1kg/processing/allPopulations_chr20_august_release.cleaned.merged.bams/ALL.cleaned.merged.list"),
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new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass),
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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 1.0, lowPass),
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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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"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 1.0, lowPass)
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)
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@ -182,8 +189,8 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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val FiltersToIgnore = List("DPFilter", "ABFilter", "ESPStandard", "QualByDepth", "StrandBias", "HomopolymerRun")
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// 1a.) Call SNPs with UG
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class snpCall (t: Target) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
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// 1.) Unified Genotyper Base
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class GenotyperBase (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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@ -191,175 +198,170 @@ class MethodsDevelopmentCallingPipeline extends QScript {
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this.stand_call_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } )
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this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } )
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this.input_file :+= t.bamList
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if (t.dbsnpFile.endsWith(".rod"))
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this.DBSNP = new File(t.dbsnpFile)
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else if (t.dbsnpFile.endsWith(".vcf"))
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this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
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}
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// 1a.) Call SNPs with UG
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class snpCall (t: Target) extends GenotyperBase {
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this.out = t.rawVCF
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this.baq = Some( if (noBAQ) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY})
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this.analysisName = t.name + "_UGs"
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this.jobName = t.name + ".snpcall"
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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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this.jobName = queueLogDir + t.name + ".snpcall"
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}
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// 1b.) Call Indels with UG
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class indelCall (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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this.dcov = Some( if ( t.isLowpass ) { 50 } else { 250 } )
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this.stand_call_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } )
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this.stand_emit_conf = Some( if ( t.isLowpass ) { 4.0 } else { 30.0 } )
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this.input_file :+= t.bamList
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class indelCall (t: Target) extends GenotyperBase {
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this.out = t.rawIndelVCF
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this.glm = Some(org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.DINDEL)
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this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF)
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this.analysisName = t.name + "_UGi"
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this.jobName = t.name + ".indelcall"
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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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this.jobName = queueLogDir + t.name + ".indelcall"
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}
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// 2a.) Filter SNPs
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class snpFilter (t: Target) extends VariantFiltration with UNIVERSAL_GATK_ARGS {
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// 2.) Hard Filtering Base
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class FilterBase (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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this.variantVCF = t.rawVCF
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this.out = t.filteredVCF
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this.filterName ++= List("HARD_TO_VALIDATE")
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this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"")
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this.analysisName = t.name + "_VF"
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this.jobName = t.name + ".snpfilter"
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if (!noMASK) {
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this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
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this.maskName = "InDel"
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}
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}
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// 2b.) Filter Indels
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class indelFilter (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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this.variantVCF = t.rawIndelVCF
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this.out = t.filteredIndelVCF
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this.filterName ++= List("HARD_TO_VALIDATE", "LowQual", "StrandBias", "QualByDepth", "HomopolymerRun")
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this.filterExpression ++= List("\"MQ0 >= 4 && (MQ0 / (1.0 * DP)) > 0.1\"", "\"QUAL<30.0\"", "\"SB>=-1.0\"", "\"QD<1.0\"", "\"HRun>=15\"")
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this.analysisName = t.name + "_VF"
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this.jobName = t.name + ".indelfilter"
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if (!noMASK) {
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// 2a.) Hard Filter for SNPs (soon to be obsolete)
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class snpFilter (t: Target) extends FilterBase {
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this.variantVCF = t.rawVCF
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this.out = t.filteredVCF
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if (useMask) {
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this.rodBind :+= RodBind("mask", "Bed", t.maskFile)
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this.maskName = "InDel"
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}
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this.analysisName = t.name + "_VF"
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this.jobName = queueLogDir + t.name + ".snpfilter"
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}
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// 2b.) Hard Filter for Indels
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class indelFilter (t: Target) extends FilterBase {
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this.variantVCF = t.rawIndelVCF
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this.out = t.filteredIndelVCF
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this.filterName ++= List("LowQual", "StrandBias", "QualByDepth", "HomopolymerRun")
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if (t.isLowpass)
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this.filterExpression ++= List("\"QUAL<30.0\"", "\"SB>=-1.0\"", "\"QD<1.0\"", "\"HRun>=15\"")
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else
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this.filterExpression ++= List("\"QUAL<50.0\"", "\"SB>=-1.0\"", "\"QD<5.0\"", "\"HRun>=15\"")
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this.analysisName = t.name + "_VF"
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this.jobName = queueLogDir + t.name + ".indelfilter"
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}
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// 3.) VQSR part1 Generate Gaussian clusters based on truth sites
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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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if( t.hapmapFile.contains("b37") )
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this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
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this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
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this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
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this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.qual = Some(350) // clustering parameters to be updated soon pending new experimentation results
|
||||
this.std = Some(3.5)
|
||||
this.mG = Some(10)
|
||||
this.ignoreFilter ++= FiltersToIgnore
|
||||
this.analysisName = name + "_GVC"
|
||||
this.jobName = t.name + ".cluster"
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
|
||||
this.reference_sequence = t.reference
|
||||
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
|
||||
if( t.hapmapFile.contains("b37") )
|
||||
this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
|
||||
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
|
||||
this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
|
||||
this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.qual = Some(350) // clustering parameters to be updated soon pending new experimentation results
|
||||
this.std = Some(3.5)
|
||||
this.mG = Some(10)
|
||||
this.ignoreFilter ++= FiltersToIgnore
|
||||
this.analysisName = name + "_GVC"
|
||||
this.jobName = queueLogDir + t.name + ".cluster"
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
}
|
||||
|
||||
// 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters
|
||||
class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
|
||||
val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
|
||||
this.reference_sequence = t.reference
|
||||
if( t.hapmapFile.contains("b37") )
|
||||
this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
|
||||
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
|
||||
this.rodBind :+= RodBind("truth", "VCF", t.hapmapFile)
|
||||
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
|
||||
this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
|
||||
this.analysisName = name + "_VR"
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.ignoreFilter ++= FiltersToIgnore
|
||||
this.ignoreFilter ++= List("HARD_TO_VALIDATE")
|
||||
this.target_titv = Some(t.titvTarget)
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name }
|
||||
this.reference_sequence = t.reference
|
||||
if( t.hapmapFile.contains("b37") )
|
||||
this.rodBind :+= RodBind("1kg", "VCF", "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf")
|
||||
this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile)
|
||||
this.rodBind :+= RodBind("truth", "VCF", t.hapmapFile)
|
||||
this.rodBind :+= RodBind("input", "VCF", if ( goldStandard ) { t.goldStandard_VCF } else { t.filteredVCF } )
|
||||
this.clusterFile = if ( goldStandard ) { t.goldStandardClusterFile } else { t.clusterFile }
|
||||
this.analysisName = name + "_VR"
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.ignoreFilter ++= FiltersToIgnore
|
||||
this.ignoreFilter ++= List("HARD_TO_VALIDATE")
|
||||
this.target_titv = Some(t.titvTarget)
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
}
|
||||
|
||||
// 4a.) Choose VQSR tranches based on novel ti/tv
|
||||
class VariantRecalibratorTiTv(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
|
||||
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
|
||||
this.out = t.titvRecalibratedVCF
|
||||
this.tranchesFile = t.titvTranchesFile
|
||||
this.jobName = t.name + ".titv"
|
||||
this.tranche ++= List("0.1", "1.0", "3.0", "5.0", "10.0", "100.0")
|
||||
this.out = t.titvRecalibratedVCF
|
||||
this.tranchesFile = t.titvTranchesFile
|
||||
this.jobName = queueLogDir + t.name + ".titv"
|
||||
}
|
||||
|
||||
// 4b.) Choose VQSR tranches based on sensitivity to truth set
|
||||
class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) {
|
||||
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY)
|
||||
this.tranche ++= List("0.1", "1.0", "10.0", "100.0")
|
||||
this.out = t.tsRecalibratedVCF
|
||||
this.priorDBSNP = Some(2.0)
|
||||
this.priorHapMap = Some(2.0)
|
||||
this.prior1KG = Some(2.0)
|
||||
this.tranchesFile = t.tsTranchesFile
|
||||
this.jobName = t.name + ".nrs"
|
||||
this.sm = Some(org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.SelectionMetricType.TRUTH_SENSITIVITY)
|
||||
this.tranche ++= List("0.1", "1.0", "3.0", "5.0", "10.0", "100.0")
|
||||
this.out = t.tsRecalibratedVCF
|
||||
this.priorDBSNP = Some(2.0)
|
||||
this.priorHapMap = Some(2.0)
|
||||
this.prior1KG = Some(2.0)
|
||||
this.tranchesFile = t.tsTranchesFile
|
||||
this.jobName = queueLogDir + t.name + ".nrs"
|
||||
}
|
||||
|
||||
// 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche
|
||||
class VariantCut(t: Target) extends ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
|
||||
this.reference_sequence = t.reference
|
||||
this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.out = t.cutVCF
|
||||
this.tranchesFile = t.tsTranchesFile
|
||||
this.fdr_filter_level = Some(1.0)
|
||||
this.analysisName = t.name + "_VC"
|
||||
this.jobName = t.name + ".cut"
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
this.reference_sequence = t.reference
|
||||
this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF )
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.out = t.cutVCF
|
||||
this.tranchesFile = t.tsTranchesFile
|
||||
this.fdr_filter_level = Some(t.trancheTarget)
|
||||
this.analysisName = t.name + "_VC"
|
||||
this.jobName = queueLogDir + t.name + ".cut"
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
}
|
||||
|
||||
// 6a.) Variant Evaluation (OPTIONAL) based on the sensitivity recalibrated vcf
|
||||
class snpEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
|
||||
val name: String = t.name
|
||||
this.reference_sequence = t.reference
|
||||
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
|
||||
this.rodBind :+= RodBind("eval", "VCF", if (!noCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
|
||||
this.analysisName = name + "_VE"
|
||||
this.jobName = t.name + ".snpeval"
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.out = t.evalFile
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
// 6.) Variant Evaluation Base(OPTIONAL)
|
||||
class EvalBase(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
|
||||
this.reference_sequence = t.reference
|
||||
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
}
|
||||
|
||||
// 6b.) Variant Evaluation of Indels (OPTIONAL)
|
||||
class indelEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
|
||||
val name: String = t.name
|
||||
this.reference_sequence = t.reference
|
||||
this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)
|
||||
this.rodBind :+= RodBind("eval", "VCF", if (!noCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
|
||||
this.analysisName = name + "_VE"
|
||||
this.jobName = t.name + ".indeleval"
|
||||
this.intervalsString ++= List(t.intervals)
|
||||
this.out = t.evalFile
|
||||
if (t.dbsnpFile.endsWith(".rod"))
|
||||
this.DBSNP = new File(t.dbsnpFile)
|
||||
else if (t.dbsnpFile.endsWith(".vcf"))
|
||||
this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
|
||||
// 6a.) SNP Evaluation (OPTIONAL) based on the cut vcf
|
||||
class snpEvaluation(t: Target) extends EvalBase {
|
||||
if (t.reference == b37 || t.reference == hg19) this.rodBind :+= RodBind("compomni", "VCF", omni_b37)
|
||||
this.rodBind :+= RodBind("eval", "VCF", if (useCut) {t.cutVCF} else {t.tsRecalibratedVCF} )
|
||||
this.evalModule :+= "GenotypeConcordance"
|
||||
this.out = t.evalFile
|
||||
this.analysisName = t.name + "_VEs"
|
||||
this.jobName = queueLogDir + t.name + ".snp.eval"
|
||||
}
|
||||
|
||||
// 6b.) Indel Evaluation (OPTIONAL)
|
||||
class indelEvaluation(t: Target) extends EvalBase {
|
||||
this.rodBind :+= RodBind("eval", "VCF", t.filteredIndelVCF)
|
||||
this.evalModule :+= "IndelStatistics"
|
||||
this.out = t.evalIndelFile
|
||||
this.analysisName = t.name + "_VEi"
|
||||
this.jobName = queueLogDir + queueLogDir + t.name + ".indel.eval"
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -26,7 +26,7 @@ class dataProcessing extends QScript {
|
|||
@Input(doc="Reference fasta file", shortName="R", required=false)
|
||||
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
|
||||
|
||||
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false) // todo -- accept any format. Not only VCF.
|
||||
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
|
||||
val dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
|
||||
|
||||
@Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false) //todo -- once vcfs are merged, this will become the only indel vcf to be used and the merged file will be the default.
|
||||
|
|
@ -51,6 +51,9 @@ class dataProcessing extends QScript {
|
|||
val dindelASNCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/ASN.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
|
||||
val dindelEURCalls: String = "/humgen/1kg/DCC/ftp/technical/working/20110126_dindel_august/EUR.dindel_august_release_merged_pilot1.20110126.sites.vcf.gz"
|
||||
|
||||
val queueLogDir: String = ".qlog/"
|
||||
|
||||
|
||||
// Simple boolean definitions for code clarity
|
||||
val knownsOnly: Boolean = true
|
||||
val intermediate: Boolean = true
|
||||
|
|
@ -59,7 +62,7 @@ class dataProcessing extends QScript {
|
|||
trait CommandLineGATKArgs extends CommandLineGATK {
|
||||
this.jarFile = qscript.GATKjar
|
||||
this.reference_sequence = qscript.reference
|
||||
this.memoryLimit = Some(8)
|
||||
this.memoryLimit = Some(4)
|
||||
this.isIntermediate = true
|
||||
}
|
||||
|
||||
|
|
@ -135,7 +138,7 @@ class dataProcessing extends QScript {
|
|||
this.rodBind :+= RodBind("indels2", "VCF", dindelAFRCalls)
|
||||
this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
|
||||
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
|
||||
this.jobName = outIntervals + ".ktarget"
|
||||
this.jobName = queueLogDir + outIntervals + ".ktarget"
|
||||
}
|
||||
|
||||
class allTargets (inBams: String, outIntervals: String) extends knownTargets(outIntervals) {
|
||||
|
|
@ -148,7 +151,7 @@ class dataProcessing extends QScript {
|
|||
this.rodBind :+= RodBind("indels3", "VCF", dindelEURCalls)
|
||||
this.rodBind :+= RodBind("indels4", "VCF", dindelASNCalls)
|
||||
if (qscript.indels != null) this.rodBind :+= RodBind("indels5", "VCF", qscript.indels)
|
||||
this.jobName = outIntervals + ".atarget"
|
||||
this.jobName = queueLogDir + outIntervals + ".atarget"
|
||||
}
|
||||
|
||||
class clean (inBams: String, tIntervals: String, outBam: String, knownsOnly: Boolean, intermediate: Boolean) extends IndelRealigner with CommandLineGATKArgs {
|
||||
|
|
@ -168,7 +171,7 @@ class dataProcessing extends QScript {
|
|||
this.baq = Some(org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY)
|
||||
this.compress = Some(0)
|
||||
this.isIntermediate = intermediate
|
||||
this.jobName = outBam + ".clean"
|
||||
this.jobName = queueLogDir + outBam + ".clean"
|
||||
if (!intermediate && !qscript.intervalString.isEmpty()) this.intervalsString ++= List(qscript.intervalString)
|
||||
if (!intermediate && qscript.intervals != null) this.intervals :+= qscript.intervals
|
||||
}
|
||||
|
|
@ -185,7 +188,7 @@ class dataProcessing extends QScript {
|
|||
this.memoryLimit = Some(6)
|
||||
this.jarFile = qscript.dedupJar
|
||||
this.isIntermediate = true
|
||||
this.jobName = outBam + ".dedup"
|
||||
this.jobName = queueLogDir + outBam + ".dedup"
|
||||
}
|
||||
|
||||
class cov (inBam: String, outRecalFile: String) extends CountCovariates with CommandLineGATKArgs {
|
||||
|
|
@ -193,7 +196,7 @@ class dataProcessing extends QScript {
|
|||
this.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
|
||||
this.input_file :+= new File(inBam)
|
||||
this.recal_file = new File(outRecalFile)
|
||||
this.jobName = outRecalFile + ".covariates"
|
||||
this.jobName = queueLogDir + outRecalFile + ".covariates"
|
||||
}
|
||||
|
||||
class recal (inBam: String, inRecalFile: String, outBam: String) extends TableRecalibration with CommandLineGATKArgs {
|
||||
|
|
@ -202,7 +205,7 @@ class dataProcessing extends QScript {
|
|||
this.recal_file = new File(inRecalFile)
|
||||
this.out = new File(outBam)
|
||||
this.index_output_bam_on_the_fly = Some(true)
|
||||
this.jobName = outBam + ".recalibration"
|
||||
this.jobName = queueLogDir + outBam + ".recalibration"
|
||||
}
|
||||
|
||||
class analyzeCovariates (inRecalFile: String, outPath: String) extends AnalyzeCovariates {
|
||||
|
|
@ -210,12 +213,12 @@ class dataProcessing extends QScript {
|
|||
this.resources = qscript.R
|
||||
this.recal_file = new File(inRecalFile)
|
||||
this.output_dir = outPath
|
||||
this.jobName = inRecalFile + ".analyze_covariates"
|
||||
this.jobName = queueLogDir + inRecalFile + ".analyze_covariates"
|
||||
}
|
||||
|
||||
class writeList(inBams: List[File], outBamList: String) extends ListWriterFunction {
|
||||
this.inputFiles = inBams
|
||||
this.listFile = new File(outBamList)
|
||||
this.jobName = outBamList + ".bamList"
|
||||
this.jobName = queueLogDir + outBamList + ".bamList"
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue