From 15a33545f4a879e56ab2c3aaddb3cd473be66820 Mon Sep 17 00:00:00 2001 From: rpoplin Date: Sat, 18 Dec 2010 22:19:14 +0000 Subject: [PATCH] Updating Methods development pipeline qscript with the bam lists for all the data sets. It is ready for people to start running with it. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4875 348d0f76-0448-11de-a6fe-93d51630548a --- .../MethodsDevelopmentCallingPipeline.scala | 55 ++++++++++++------- 1 file changed, 35 insertions(+), 20 deletions(-) diff --git a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala index 46b30e168..3f38f457d 100755 --- a/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/rpoplin/MethodsDevelopmentCallingPipeline.scala @@ -3,7 +3,6 @@ import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction import org.broadinstitute.sting.queue.QScript import org.apache.commons.io.FilenameUtils; -import scala.io.Source._ class MethodsDevelopmentCallingPipeline extends QScript { qscript => @@ -19,7 +18,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(4); } - class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: Option[String], val titvTarget: Double) { + class Target(val baseName: String, val reference: File, val rodName: String, val bamList: File, val goldStandard_VCF: File, val intervals: String, val titvTarget: Double) { def name = qscript.outputDir + baseName def clusterFile = new File(name + ".clusters") def rawVCF = new File(name + ".raw.vcf") @@ -30,23 +29,39 @@ class MethodsDevelopmentCallingPipeline extends QScript { val hg18 = new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta") val b36 = new File("/humgen/1kg/reference/human_b36_both.fasta") - val hg19 = new File("/seq/references/Homo_sapiens_assembly19/v0/Homo_sapiens_assembly19.fasta") + val b37 = new File("/humgen/1kg/reference/human_g1k_v37.fasta") - //val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18", new File("BAM LIST HERE"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.vcf"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals"), 2.07) - //val WEx = new Target("NA12878.WEx", hg18, "hg18", new File("BAM LIST HERE"), new File("/home/radon01/depristo/work/oneOffProjects/1000GenomesProcessingPaper/wgs.v13/GA2.WEx.cleaned.ug.snpfiltered.indelfiltered.vcf"), Some("/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) - //val LowPassN60 = new Target("lowpass.N60", b36, "b36", new File("BAM LIST HERE"), new File("/home/radon01/depristo/work/oneOffProjects/VQSRCutByNRS/lowpass.N60.chr20.filtered.vcf"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"), 2.3) - //val LowPassAugust = new Target("ALL.august.v4", hg19, "b37", new File("BAM LIST HERE"), 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"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"), 2.3) - val LowPassFIN79Nov = new Target("FIN.nov2010.v4", hg19, "b37", 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"), Some("/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals"), 2.3) - //val TGPWExFH = new Target("1000G.WEx.FH", hg19, "b37", new File("BAM LIST HERE"), new File("/humgen/gsa-pipeline/PQ7LC/all_batches_v006/Plate_1/SnpCalls/Barcoded_1000G_WEx_Plate_1.cleaned.annotated.handfiltered.vcf"), Some("/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) - //val TGPWExGdA = new Target("1000G.WEx.GdA", hg19, "b37", new File("BAM LIST HERE"), new File("/humgen/gsa-scr1/delangel/NewUG/calls/AugustRelease.filtered_Q50_QD5.0_SB0.0.allSamples.SNPs_hg19.WEx_UG_newUG_MQC.vcf"), Some("/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) - - //val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, TGPWExFH, TGPWExGdA) - val targets = List(LowPassFIN79Nov) + // Define the target datasets here + val HiSeq = new Target("NA12878.HiSeq", hg18, "hg18", + new File("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.GA2.WGS.bwa.cleaned.bam"), + 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", 2.07) + val WEx = new Target("NA12878.WEx", hg18, "hg18", + 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"), + "/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) + val LowPassN60 = new Target("lowpass.N60", b36, "b36", // which reference the data is aligned to + 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 compare against + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3) // chunked interval list to use with Queue's scatter/gather functionality + val LowPassAugust = new Target("ALL.august.v4", b37, "b37", + new File("/humgen/1kg/processing/allPopulations_chr20_august_release.cleaned.merged.bams/ALL.cleaned.merged.list"), + new File("/humgen/gsa-hpprojects/dev/data/AugChr20Calls_v4_3state/ALL.august.v4.chr20.filtered.vcf"), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3) + val LowPassFIN79Nov = new Target("FIN.nov2010", b37, "b37", + 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 ** + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3) + val TGPWExGdA = new Target("1000G.WEx.GdA", b37, "b37", + new File("/humgen/1kg/processing/pipeline_test_bams/Barcoded_1000G_WEx_Reduced_Plate_1.cleaned.list"), + 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) + val targets = List(HiSeq, WEx, LowPassN60, LowPassAugust, LowPassFIN79Nov, TGPWExGdA) + def script = { def goldStandard = true for (target <- targets) { - if( !skipCalling ) { add(new UnifiedGenotyper(target)) add(new VariantFiltration(target)) @@ -69,9 +84,9 @@ class MethodsDevelopmentCallingPipeline extends QScript { class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS { this.reference_sequence = t.reference this.DBSNP = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_129_" + t.rodName + ".rod") - if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get) + this.intervalsString ++= List(t.intervals) this.scatterCount = 50 - this.dcov = Some(50) + this.dcov = Some(250) this.input_file :+= t.bamList this.out = t.rawVCF this.analysisName = t.name + "_UG" @@ -80,7 +95,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { // 2.) Filter SNPs class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration with UNIVERSAL_GATK_ARGS { this.reference_sequence = t.reference - if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get) + this.intervalsString ++= List(t.intervals) this.scatterCount = 10 this.variantVCF = t.rawVCF this.out = t.filteredVCF @@ -107,7 +122,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { } this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") this.analysisName = name + "_GVC" - if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get) + this.intervalsString ++= List(t.intervals) this.qual = Some(300) this.std = Some(3.5) this.mG = Some(16) // v2 calls @@ -132,7 +147,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { this.clusterFile = t.clusterFile } this.analysisName = name + "_VR" - if ( t.intervals != None ) this.intervalsString ++= List(t.intervals.get) + this.intervalsString ++= List(t.intervals) this.ignoreFilter ++= FiltersToIgnore this.ignoreFilter ++= List("HARD_TO_VALIDATE") this.priorDBSNP = Some(2.0) @@ -150,7 +165,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { // 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("50", "25", "10", "5", "2", "1", "0.5", "0.1") + this.tranche ++= List("0.1", "1.0", "10.0", "100.0") this.out = new File(this.name + ".ts.recalibrated.vcf") this.tranchesFile = new File(this.name + ".ts.tranches") }