diff --git a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala index edf18dba0..928c6666d 100755 --- a/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala +++ b/scala/qscript/core/MethodsDevelopmentCallingPipeline.scala @@ -1,4 +1,4 @@ -import org.broadinstitute.sting.gatk.CommandLineGATK +import org.broadinstitute.sting.queue.extensions.gatk.CommandLineGATK import org.broadinstitute.sting.queue.extensions.gatk._ import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.gatk.phonehome.GATKRunReport @@ -285,7 +285,8 @@ class MethodsDevelopmentCallingPipeline extends QScript { class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.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("hapmap", "VCF", t.hapmapFile) + this.knownName ++= List("hapmap") this.rodBind :+= RodBind("eval", "VCF", if (!noCut) {t.cutVCF} else {t.tsRecalibratedVCF} ) this.analysisName = name + "_VE" this.intervalsString ++= List(t.intervals) @@ -293,7 +294,7 @@ class MethodsDevelopmentCallingPipeline extends QScript { this.out = t.evalFile if (t.dbsnpFile.endsWith(".rod")) this.DBSNP = new File(t.dbsnpFile) - else if (t.dbsnpFile.endsWith(".vcf")) + else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) } } diff --git a/scala/qscript/oneoffs/carneiro/pbCalling.scala b/scala/qscript/oneoffs/carneiro/pbCalling.scala index 6141855ed..1d31216db 100755 --- a/scala/qscript/oneoffs/carneiro/pbCalling.scala +++ b/scala/qscript/oneoffs/carneiro/pbCalling.scala @@ -20,9 +20,6 @@ class pbCalling extends QScript { - - trait UNIVERSAL_GATK_ARGS extends CommandLineGATK { logging_level = "INFO"; jarFile = gatkJarFile; memoryLimit = Some(3); } - class Target( val baseName: String, val reference: File, @@ -33,7 +30,8 @@ class pbCalling extends QScript { val goldStandard_VCF: File, val intervals: String, val titvTarget: Double, - val isLowpass: Boolean) { + val isLowpass: Boolean, + val isCCS: Boolean) { val name = qscript.outputDir + baseName val clusterFile = new File(name + ".clusters") val rawVCF = new File(name + ".raw.vcf") @@ -73,62 +71,63 @@ class pbCalling extends QScript { // produce Kiran's Venn plots based on comparison between new VCF and gold standard produced VCF val lowPass: Boolean = true + val ccs: Boolean = true val targetDataSets: Map[String, Target] = Map( "HiSeq" -> new Target("NA12878.HiSeq", hg18, dbSNP_hg18, hapmap_hg18, "/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("/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, !lowPass), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.hg18.intervals", 2.07, !lowPass, !ccs), "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/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, lowPass), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass, !ccs), "WEx" -> new Target("NA12878.WEx", hg18, dbSNP_hg18, hapmap_hg18, "/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("/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, !lowPass), + "/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, !ccs), "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/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, !lowPass), + "/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, !ccs), "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("/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, lowPass), // chunked interval list to use with Queue's scatter/gather functionality + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.b36.intervals", 2.3, lowPass, !ccs), // chunked interval list to use with Queue's scatter/gather functionality "LowPassAugust" -> new Target("ALL.august.v4", b37, dbSNP_b37, hapmap_b37, indelMask_b37, // BUGBUG: kill this, it is too large 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, lowPass), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass, !ccs), "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/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, lowPass), + "/humgen/1kg/processing/pipeline_test_bams/whole_genome_chunked.chr20.hg19.intervals", 2.3, lowPass, !ccs), "WExTrio" -> new Target("NA12878Trio.WEx", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WEx.bwa.cleaned.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/trio/snps/NA12878Trio.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", 2.6, !lowPass), + "/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, !ccs), "pacbio" -> new Target("pacbio", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pacbio.filtered.vcf"), - "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals", 1.8, !lowPass), + "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals", 1.8, !lowPass, !ccs), "pb200" -> new Target("pb200", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pb200.filtered.vcf"), - "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.hg19.intervals", 1.8, !lowPass), + "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.hg19.intervals", 1.8, !lowPass, !ccs), "pb2k" -> new Target("pb2k", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pb2k.filtered.vcf"), - "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.hg19.intervals", 1.8, !lowPass), + "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.hg19.intervals", 1.8, !lowPass, !ccs), "cc200" -> new Target("cc200", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/cc200.filtered.vcf"), - "/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.hg19.intervals", 1.8, !lowPass), + "/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.hg19.intervals", 1.8, !lowPass, ccs), "cc2k" -> new Target("cc2k", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37, new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.recal.bam"), new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/cc2k.filtered.vcf"), - "/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.hg19.intervals", 1.8, !lowPass) + "/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.hg19.intervals", 1.8, !lowPass, ccs) ) @@ -160,7 +159,8 @@ class pbCalling extends QScript { val FiltersToIgnore = List("DPFilter", "ABFilter", "ESPStandard", "QualByDepth", "StrandBias", "HomopolymerRun") // 1.) Call SNPs with UG - class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper with UNIVERSAL_GATK_ARGS { + class UnifiedGenotyper(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.UnifiedGenotyper { + this.jarFile = gatkJarFile this.reference_sequence = t.reference this.intervalsString ++= List(t.intervals) this.scatterCount = 63 // the smallest interval list has 63 intervals, one for each Mb on chr20 @@ -176,13 +176,13 @@ class pbCalling extends QScript { else if (t.dbsnpFile.endsWith(".vcf")) this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile) // Ridiculous workaround to get pacbio data to run.. never commit this! - this.assume_single_sample_reads = "NA12878" - this.deletions = Some(0.5) - this.mbq = Some(10) + this.deletions = Some(0.5) + this.mbq = Some(10) } // 2.) Filter SNPs - class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration with UNIVERSAL_GATK_ARGS { + class VariantFiltration(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantFiltration { + this.jarFile = gatkJarFile this.reference_sequence = t.reference this.intervalsString ++= List(t.intervals) this.scatterCount = 10 @@ -194,7 +194,8 @@ class pbCalling extends QScript { } // 3.) VQSR part1 Generate Gaussian clusters based on truth sites - class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters with UNIVERSAL_GATK_ARGS { + class GenerateVariantClusters(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.GenerateVariantClusters { + this.jarFile = gatkJarFile val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name } this.reference_sequence = t.reference this.rodBind :+= RodBind("hapmap", "VCF", t.hapmapFile) @@ -202,7 +203,10 @@ class pbCalling extends QScript { 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") + if (t.isCCS) + this.use_annotation ++= List("QD", "HaplotypeScore", "HRun") + else + this.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") this.analysisName = name + "_GVC" this.intervalsString ++= List(t.intervals) this.qual = Some(350) // clustering parameters to be updated soon pending new experimentation results @@ -216,7 +220,8 @@ class pbCalling extends QScript { } // 4.) VQSR part2 Calculate new LOD for all input SNPs by evaluating the Gaussian clusters - class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator with UNIVERSAL_GATK_ARGS { + class VariantRecalibratorBase(t: Target, goldStandard: Boolean) extends org.broadinstitute.sting.queue.extensions.gatk.VariantRecalibrator { + this.jarFile = gatkJarFile val name: String = if ( goldStandard ) { t.goldStandardName } else { t.name } this.reference_sequence = t.reference if( t.hapmapFile.contains("b37") ) @@ -238,6 +243,7 @@ class pbCalling extends QScript { // 4a.) Choose VQSR tranches based on novel ti/tv class VariantRecalibratorTiTv(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) { + this.jarFile = gatkJarFile this.tranche ++= List("0.1", "1.0", "10.0", "100.0") this.out = t.titvRecalibratedVCF this.tranchesFile = t.titvTranchesFile @@ -245,6 +251,7 @@ class pbCalling extends QScript { // 4b.) Choose VQSR tranches based on sensitivity to truth set class VariantRecalibratorNRS(t: Target, goldStandard: Boolean) extends VariantRecalibratorBase(t, goldStandard) { + this.jarFile = gatkJarFile 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 @@ -255,7 +262,8 @@ class pbCalling extends QScript { } // 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche - class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts with UNIVERSAL_GATK_ARGS { + class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts { + this.jarFile = gatkJarFile this.reference_sequence = t.reference this.rodBind :+= RodBind("input", "VCF", t.tsRecalibratedVCF ) this.analysisName = t.name + "_VC" @@ -270,10 +278,11 @@ class pbCalling extends QScript { } // 6.) Variant Evaluation based on the sensitivity recalibrated vcf - class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS { + class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval { + this.jarFile = gatkJarFile val name: String = t.name this.reference_sequence = t.reference - this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile) + this.rodBind :+= RodBind("comp", "VCF", t.hapmapFile) this.rodBind :+= RodBind("eval", "VCF", t.cutVCF) this.analysisName = name + "_VE" this.intervalsString ++= List(t.intervals)