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Updated MDCP with INDEL best practices 

* chose 90.0 indel cut target for most datasets (this is arbitrary).
This commit is contained in:
Mauricio Carneiro 2012-01-04 12:05:08 -05:00
parent 65c614fb4b
commit f6a18aea63
1 changed files with 103 additions and 63 deletions
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166
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/MethodsDevelopmentCallingPipeline.scala
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@ -46,20 +46,24 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val bamList: File, val bamList: File,
val goldStandard_VCF: File, val goldStandard_VCF: File,
val intervals: String, val intervals: String,
val titvTarget: Double, val indelTranchTarget: Double,
val trancheTarget: Double, val snpTrancheTarget: Double,
val isLowpass: Boolean, val isLowpass: Boolean,
val isExome: Boolean, val isExome: Boolean,
val nSamples: Int) { val nSamples: Int) {
val name = qscript.outputDir + baseName val name = qscript.outputDir + baseName
val clusterFile = new File(name + ".clusters") val clusterFile = new File(name + ".clusters")
val rawVCF = new File(name + ".raw.vcf") val rawSnpVCF = new File(name + ".raw.vcf")
val rawIndelVCF = new File(name + ".raw.indel.vcf") val rawIndelVCF = new File(name + ".raw.indel.vcf")
val filteredIndelVCF = new File(name + ".filtered.indel.vcf") val filteredIndelVCF = new File(name + ".filtered.indel.vcf")
val recalibratedVCF = new File(name + ".recalibrated.vcf") val recalibratedSnpVCF = new File(name + ".snp.recalibrated.vcf")
val tranchesFile = new File(name + ".tranches") val recalibratedIndelVCF = new File(name + ".indel.recalibrated.vcf")
val vqsrRscript = name + ".vqsr.r" val tranchesSnpFile = new File(name + ".snp.tranches")
val recalFile = new File(name + ".tranches.recal") val tranchesIndelFile = new File(name + ".indel.tranches")
val vqsrSnpRscript = name + ".snp.vqsr.r"
val vqsrIndelRscript = name + ".indel.vqsr.r"
val recalSnpFile = new File(name + ".snp.tranches.recal")
val recalIndelFile = new File(name + ".indel.tranches.recal")
val goldStandardRecalibratedVCF = new File(name + "goldStandard.recalibrated.vcf") val goldStandardRecalibratedVCF = new File(name + "goldStandard.recalibrated.vcf")
val goldStandardTranchesFile = new File(name + "goldStandard.tranches") val goldStandardTranchesFile = new File(name + "goldStandard.tranches")
val goldStandardRecalFile = new File(name + "goldStandard.tranches.recal") val goldStandardRecalFile = new File(name + "goldStandard.tranches.recal")
@ -88,6 +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 lowPass: Boolean = true val lowPass: Boolean = true
val exome: Boolean = true val exome: Boolean = true
@ -101,69 +106,69 @@ class MethodsDevelopmentCallingPipeline extends QScript {
"NA12878_gold" -> new Target("NA12878.goldStandard", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, "NA12878_gold" -> new Target("NA12878.goldStandard", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/data/goldStandard.list"), new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/data/goldStandard.list"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** There is no gold standard for the gold standard ** new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** There is no gold standard for the gold standard **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, lowPass, !exome, 391), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 90.0, 99.0, lowPass, !exome, 391),
"NA12878_wgs_b37" -> new Target("NA12878.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, "NA12878_wgs_b37" -> new Target("NA12878.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 1),
"NA12878_wgs_decoy" -> new Target("NA12878.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, "NA12878_wgs_decoy" -> new Target("NA12878.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.NA12878.clean.dedup.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.HiSeq19.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.noChrY.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 1),
"NA12878_wgs_hg18" -> new Target("NA12878.HiSeq.WGS.hg18", hg18, dbSNP_hg18_129, hapmap_hg18, "NA12878_wgs_hg18" -> new Target("NA12878.HiSeq.WGS.hg18", hg18, dbSNP_hg18_129, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask", "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.indels.10.mask",
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam"),
new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.14, 99.0, !lowPass, !exome, 1), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 90.0, 99.0, !lowPass, !exome, 1),
"NA12878_wex_b37" -> new Target("NA12878.HiSeq.WEx.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, "NA12878_wex_b37" -> new Target("NA12878.HiSeq.WEx.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/seq/picard_aggregation/C339/NA12878/v3/NA12878.bam"), new File("/seq/picard_aggregation/C339/NA12878/v3/NA12878.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/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", 3.3, 98.0, !lowPass, exome, 1), "/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", 90.0, 98.0, !lowPass, exome, 1),
"NA12878_wex_hg18" -> new Target("NA12878.HiSeq.WEx.hg18", hg18, dbSNP_hg18_129, hapmap_hg18, "NA12878_wex_hg18" -> new Target("NA12878.HiSeq.WEx.hg18", hg18, dbSNP_hg18_129, hapmap_hg18,
"/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask", "/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.indels.10.mask",
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.WEx.cleaned.recal.bam"),
new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"),
"/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 3.3, 98.0, !lowPass, exome, 1), "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.targets.interval_list", 90.0, 98.0, !lowPass, exome, 1),
"NA12878_wex_decoy" -> new Target("NA12878.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, "NA12878_wex_decoy" -> new Target("NA12878.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.NA12878.clean.dedup.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.NA12878.clean.dedup.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/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", 3.3, 98.0, !lowPass, exome, 1), "/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", 90.0, 98.0, !lowPass, exome, 1),
"CEUTrio_wex_b37" -> new Target("CEUTrio.HiSeq.WEx.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, "CEUTrio_wex_b37" -> new Target("CEUTrio.HiSeq.WEx.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"),
"/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", 3.3, 98.0, !lowPass, exome, 3), "/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", 90.0, 98.0, !lowPass, exome, 3),
"CEUTrio_wgs_b37" -> new Target("CEUTrio.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, "CEUTrio_wgs_b37" -> new Target("CEUTrio.HiSeq.WGS.b37", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.bwa.cleaned.recal.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 3),
"CEUTrio_wex_decoy" -> new Target("CEUTrio.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, "CEUTrio_wex_decoy" -> new Target("CEUTrio.HiSeq.WEx.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.list"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.b37_decoy.list"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/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", 3.3, 98.0, !lowPass, exome, 3), "/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", 90.0, 98.0, !lowPass, exome, 3),
"CEUTrio_wgs_decoy" -> new Target("CEUTrio.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37, "CEUTrio_wgs_decoy" -> new Target("CEUTrio.HiSeq.WGS.b37_decoy", b37_decoy, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.list"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37_decoy.list"),
new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/carneiro/trio/analysis/snps/CEUTrio.WEx.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.3, 99.0, !lowPass, !exome, 3), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 3),
"GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37, hapmap_b37, indelMask_b37, "GA2hg19" -> new Target("NA12878.GA2.hg19", hg19, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"), new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.hg19.bam"),
new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.GA2.hg19.filtered.vcf"), new File("/humgen/gsa-hpprojects/dev/carneiro/NA12878/analysis/snps/NA12878.GA2.hg19.filtered.vcf"),
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 2.14, 99.0, !lowPass, !exome, 1), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg19.intervals", 90.0, 99.0, !lowPass, !exome, 1),
"FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37, "FIN" -> new Target("FIN", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"), new File("/humgen/1kg/processing/pipeline_test_bams/FIN.79sample.Nov2010.chr20.bam"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 99.0, lowPass, !exome, 79), "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 90.0, 99.0, lowPass, !exome, 79),
"TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_b37, "TGPWExGdA" -> new Target("1000G.WEx.GdA", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), // BUGBUG: reduce from 60 to 20 people
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 ** 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 **
"/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, 99.0, !lowPass, exome, 96), "/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", 90.0, 99.0, !lowPass, exome, 96),
"LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36, "LowPassN60" -> new Target("lowpass.N60", b36, dbSNP_b36, hapmap_b36, indelMask_b36,
new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from new File("/humgen/1kg/analysis/bamsForDataProcessingPapers/lowpass_b36/lowpass.chr20.cleaned.matefixed.bam"), // the bam list to call from
new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), // the gold standard VCF file to run through the VQSR new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), // the gold standard VCF file to run through the VQSR
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, 99.0, lowPass, !exome, 60), // chunked interval list to use with Queue's scatter/gather functionality "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 90.0, 99.0, lowPass, !exome, 60), // chunked interval list to use with Queue's scatter/gather functionality
"LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_b37, "LowPassEUR363Nov" -> new Target("EUR.nov2010", b37, dbSNP_b37, hapmap_b37, indelMask_b37,
new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"), new File("/humgen/1kg/processing/pipeline_test_bams/EUR.363sample.Nov2010.chr20.bam"),
new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED ** new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), // ** THIS GOLD STANDARD NEEDS TO BE CORRECTED **
"/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, 99.0, lowPass, !exome, 363) "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 90.0, 99.0, lowPass, !exome, 363)
) )
@ -181,15 +186,15 @@ class MethodsDevelopmentCallingPipeline extends QScript {
val goldStandard = true val goldStandard = true
for (target <- targets) { for (target <- targets) {
if( !skipCalling ) { if( !skipCalling ) {
if (!noIndels) add(new indelCall(target), new indelFilter(target), new indelEvaluation(target)) if (!noIndels) add(new indelCall(target), new indelRecal(target), new indelCut(target), new indelEvaluation(target))
add(new snpCall(target)) add(new snpCall(target))
add(new VQSR(target, !goldStandard)) add(new snpRecal(target, !goldStandard))
add(new applyVQSR(target, !goldStandard)) add(new snpCut(target, !goldStandard))
add(new snpEvaluation(target)) add(new snpEvaluation(target))
} }
if ( runGoldStandard ) { if ( runGoldStandard ) {
add(new VQSR(target, goldStandard)) add(new snpRecal(target, goldStandard))
add(new applyVQSR(target, goldStandard)) add(new snpCut(target, goldStandard))
} }
} }
} }
@ -222,7 +227,7 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.min_base_quality_score = minimumBaseQuality this.min_base_quality_score = minimumBaseQuality
if (qscript.deletions >= 0) if (qscript.deletions >= 0)
this.max_deletion_fraction = qscript.deletions this.max_deletion_fraction = qscript.deletions
this.out = t.rawVCF this.out = t.rawSnpVCF
this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP this.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.SNP
this.baq = if (noBAQ || t.isExome) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY} this.baq = if (noBAQ || t.isExome) {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.OFF} else {org.broadinstitute.sting.utils.baq.BAQ.CalculationMode.CALCULATE_AS_NECESSARY}
this.analysisName = t.name + "_UGs" this.analysisName = t.name + "_UGs"
@ -257,79 +262,114 @@ class MethodsDevelopmentCallingPipeline extends QScript {
this.jobName = queueLogDir + t.name + ".indelfilter" this.jobName = queueLogDir + t.name + ".indelfilter"
} }
// 3.) Variant Quality Score Recalibration - Generate Recalibration table class VQSRBase(t: Target) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
class VQSR(t: Target, goldStandard: Boolean) extends VariantRecalibrator with UNIVERSAL_GATK_ARGS {
this.nt = 2 this.nt = 2
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.input :+= ( if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } ) this.allPoly = true
this.resource :+= new TaggedFile( t.hapmapFile, "training=true,truth=true,prior=15.0" ) 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.resource :+= new TaggedFile( omni_b37, "training=true,truth=true,prior=12.0" ) }
this.resource :+= new TaggedFile( training_1000G, "training=true,prior=10.0" )
class snpRecal(t: Target, goldStandard: Boolean) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS {
this.input :+= ( if ( goldStandard ) { t.goldStandard_VCF } else { t.rawSnpVCF } )
this.resource :+= new TaggedFile( t.hapmapFile, "known=false,training=true,truth=true,prior=15.0" )
this.resource :+= new TaggedFile( omni_b37, "known=false,training=true,truth=true,prior=12.0" )
this.resource :+= new TaggedFile( training_1000G, "known=false,training=true,prior=10.0" )
this.resource :+= new TaggedFile( t.dbsnpFile, "known=true,prior=2.0" ) this.resource :+= new TaggedFile( t.dbsnpFile, "known=true,prior=2.0" )
this.resource :+= new TaggedFile( projectConsensus_1000G, "prior=8.0" ) this.resource :+= new TaggedFile( projectConsensus_1000G, "prior=8.0" )
this.use_annotation ++= List("QD", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "MQ", "FS") this.use_annotation ++= List("QD", "HaplotypeScore", "MQRankSum", "ReadPosRankSum", "MQ", "FS")
if(t.nSamples >= 10) { // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate if(t.nSamples >= 10)
this.use_annotation ++= List("InbreedingCoeff") this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate
} if(!t.isExome)
if(!t.isExome) {
this.use_annotation ++= List("DP") this.use_annotation ++= List("DP")
} else { // exome specific parameters else { // exome specific parameters
this.resource :+= new TaggedFile( badSites_1000G, "bad=true,prior=2.0" ) this.resource :+= new TaggedFile( badSites_1000G, "bad=true,prior=2.0" )
this.mG = 6 this.mG = 6
if(t.nSamples <= 3) { // very few exome samples means very few variants if(t.nSamples <= 3) { // very few exome samples means very few variants
this.mG = 4 this.mG = 4
this.percentBad = 0.04 this.percentBad = 0.04
} }
} }
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile } this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesSnpFile }
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile } this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalSnpFile }
this.allPoly = true this.rscript_file = t.vqsrSnpRscript
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.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
this.rscript_file = t.vqsrRscript this.analysisName = t.name + "_VQSRs"
this.analysisName = t.name + "_VQSR" this.jobName = queueLogDir + t.name + ".snprecal"
this.jobName = queueLogDir + t.name + ".VQSR"
} }
class indelRecal(t: Target) extends VQSRBase(t) with UNIVERSAL_GATK_ARGS {
this.input :+= t.rawIndelVCF
this.resource :+= new TaggedFile( millsDevine_b37, "known=true,training=true,truth=true,prior=12.0" )
this.use_annotation ++= List("QD", "HaplotypeScore", "ReadPosRankSum", "FS")
if(t.nSamples >= 10)
this.use_annotation ++= List("InbreedingCoeff") // InbreedingCoeff is a population-wide statistic that requires at least 10 samples to calculate
this.tranches_file = t.tranchesIndelFile
this.recal_file = t.recalIndelFile
this.rscript_file = t.vqsrIndelRscript
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
this.analysisName = t.name + "_VQSRi"
this.jobName = queueLogDir + t.name + ".indelrecal"
}
// 4.) Apply the recalibration table to the appropriate tranches // 4.) Apply the recalibration table to the appropriate tranches
class applyVQSR (t: Target, goldStandard: Boolean) extends ApplyRecalibration with UNIVERSAL_GATK_ARGS { class applyVQSRBase (t: Target) extends ApplyRecalibration with UNIVERSAL_GATK_ARGS {
this.memoryLimit = 6 this.memoryLimit = 6
this.reference_sequence = t.reference this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals) this.intervalsString ++= List(t.intervals)
this.input :+= ( if ( goldStandard ) { t.goldStandard_VCF } else { t.rawVCF } )
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesFile}
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalFile }
this.ts_filter_level = t.trancheTarget
this.out = t.recalibratedVCF
this.analysisName = t.name + "_AVQSR"
this.jobName = queueLogDir + t.name + ".applyVQSR"
} }
class snpCut (t: Target, goldStandard: Boolean) extends applyVQSRBase(t) {
this.input :+= ( if ( goldStandard ) { t.goldStandard_VCF } else { t.rawSnpVCF } )
this.tranches_file = if ( goldStandard ) { t.goldStandardTranchesFile } else { t.tranchesSnpFile}
this.recal_file = if ( goldStandard ) { t.goldStandardRecalFile } else { t.recalSnpFile }
this.ts_filter_level = t.snpTrancheTarget
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.SNP
this.out = t.recalibratedSnpVCF
this.analysisName = t.name + "_AVQSRs"
this.jobName = queueLogDir + t.name + ".snpcut"
}
class indelCut (t: Target) extends applyVQSRBase(t) {
this.input :+= t.rawIndelVCF
this.tranches_file = t.tranchesIndelFile
this.recal_file = t.recalIndelFile
this.ts_filter_level = t.indelTranchTarget
this.mode = org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorArgumentCollection.Mode.INDEL
this.out = t.recalibratedIndelVCF
this.analysisName = t.name + "_AVQSRi"
this.jobName = queueLogDir + t.name + ".indelcut"
}
// 5.) Variant Evaluation Base(OPTIONAL) // 5.) Variant Evaluation Base(OPTIONAL)
class EvalBase(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS { class EvalBase(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
this.memoryLimit = 3 this.memoryLimit = 3
this.reference_sequence = t.reference
this.comp :+= new TaggedFile(t.hapmapFile, "hapmap" ) this.comp :+= new TaggedFile(t.hapmapFile, "hapmap" )
this.intervalsString ++= List(t.intervals)
this.D = new File(t.dbsnpFile) this.D = new File(t.dbsnpFile)
this.reference_sequence = t.reference
this.intervalsString ++= List(t.intervals)
this.sample = samples this.sample = samples
} }
// 5a.) SNP Evaluation (OPTIONAL) based on the cut vcf // 5a.) SNP Evaluation (OPTIONAL) based on the cut vcf
class snpEvaluation(t: Target) extends EvalBase(t) { class snpEvaluation(t: Target) extends EvalBase(t) {
if (t.reference == b37 || t.reference == hg19) this.comp :+= new TaggedFile( omni_b37, "omni" ) if (t.reference == b37 || t.reference == hg19) this.comp :+= new TaggedFile( omni_b37, "omni" )
this.eval :+= t.recalibratedVCF this.eval :+= t.recalibratedSnpVCF
this.out = t.evalFile this.out = t.evalFile
this.analysisName = t.name + "_VEs" this.analysisName = t.name + "_VEs"
this.jobName = queueLogDir + t.name + ".snp.eval" this.jobName = queueLogDir + t.name + ".snpeval"
} }
// 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.filteredIndelVCF this.eval :+= t.recalibratedIndelVCF
this.evalModule :+= "IndelStatistics" this.comp :+= new TaggedFile(millsDevine_b37, "mills" )
this.noEV = true
this.evalModule = List("CompOverlap", "CountVariants", "TiTvVariantEvaluator", "ValidationReport", "IndelStatistics")
this.out = t.evalIndelFile this.out = t.evalIndelFile
this.analysisName = t.name + "_VEi" this.analysisName = t.name + "_VEi"
this.jobName = queueLogDir + queueLogDir + t.name + ".indel.eval" this.jobName = queueLogDir + queueLogDir + t.name + ".indeleval"
} }
} }