calling pipeline for v13 of the paper calls -- the final version
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4716 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo
parent
28805d17ca
commit
187b464ded
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@ -12,7 +12,7 @@ import string
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from madPipelineUtils import *
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EXCLUDE_CHRS = ['chrM', 'chrY']
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EXTRA_GATK_ARGS = ' -XL chrM -XL chrY -L chr1 ' # -XL chrX -XL chrY '
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EXTRA_GATK_ARGS = ' -XL chrM -XL chrY ' # -XL chrX -XL chrY '
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#EXTRA_GATK_ARGS = ' -XL chrM -XL chrY ' # -XL chrX -XL chrY '
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VALIDATION_DIR = '/humgen/gsa-hpprojects/GATK/data/Comparisons'
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BAM_ROOT = '/humgen/1kg/analysis/bamsForDataProcessingPapers/'
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@ -20,10 +20,10 @@ WE_LIST = '/seq/references/HybSelOligos/whole_exome_agilent_designed_120/whole_e
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WGS_FILTER = [['ABFilter', 'AB > 0.75 && DP > 40'], ['DPFilter', 'DP > 120 || SB > -0.10']] # , ['QDFilter', 'QD < 5.0 && DP > 40']]
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WE_FILTER = [['ESPStandard', 'AB > 0.75 || QD < 5.0 || HRun > 3 || SB > -0.10']]
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UG_ARGS = "-mbq 20 -mmq 20 -stand_call_conf 30 -stand_emit_conf 10 -hets 0.78e-3 -mrl 10000"
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UG_ARGS = "-mbq 20 -mmq 20 -stand_call_conf 50 -stand_emit_conf 10 -hets 0.78e-3 -dcov 10000 -pnrm GRID_SEARCH"
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class CallTarget:
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def __init__(self, name, bam, interval = '', callArgs = "", b36 = False, optimize = True, filters = [], targetTiTv = 2.07, maxClusters = 16, minQual = 300, tranchToTake = 0.1):
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def __init__(self, name, bam, interval = '', callArgs = "", b36 = False, optimize = True, filters = [], targetTiTv = 2.07, maxClusters = 16, minQual = 300, tranchToTake = 1):
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self.name = name
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self.bam = bam
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self.interval = interval
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@ -68,7 +68,8 @@ TECH_COMP = '/humgen/gsa-hphome1/kiran/one_off_projects/multiTechComparisons/res
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#WGS_INTERVAL = '-L chr1:1-50,000,000'
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def weTarget(name, bam, ignore = '', args = '', filters = None):
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return CallTarget(name, bam, interval = WE_LIST, callArgs = args, filters = WE_FILTER, targetTiTv = 3.0, maxClusters = 8, minQual = 2800, tranchToTake = 10)
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# 3.0 was old target, new is 2.8
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return CallTarget(name, bam, interval = WE_LIST, callArgs = args, filters = WE_FILTER, targetTiTv = 2.8, maxClusters = 12, minQual = 2800, tranchToTake = 10)
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#TARGETS_BY_STRATEGY = [['', ''], ['.OQ', '-OQ'], ['.OQ.noCM', '-OQ -bm THREE_STATE'], ['.noCM', '-bm THREE_STATE']]
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TARGETS_BY_STRATEGY = [['', ''], ['.OQ', '-OQ']]
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@ -144,16 +145,15 @@ def main():
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# HiSeq
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targets += targetsByStrategy(CallTarget, 'HiSeq.WGS.raw', '/seq/dirseq/pem/seq/picard_aggregation/G2946/NA12878/v1/NA12878.bam', WGS_INTERVAL, filters = WGS_FILTER)
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targets += targetsByStrategy(CallTarget, 'HiSeq.WGS.cleaned', '/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/tmp.list', WGS_INTERVAL, filters = WGS_FILTER)
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#targets += targetsByStrategy(CallTarget, 'HiSeq.WGS.cleaned', '/humgen/1kg/analysis/bamsForDataProcessingPapers/highpass_v3/NA12878.HiSeq.WGS.bwa.cleaned.bam', WGS_INTERVAL, filters = WGS_FILTER)
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# targets += targetsByStrategy(CallTarget, 'HiSeq.WGS.cleaned', BAM_ROOT + '/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam', WGS_INTERVAL, filters = WGS_FILTER)
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#targets += targetsByStrategy(CallTarget, 'HiSeq.WGS.cleaned', '/humgen/1kg/analysis/bamsForDataProcessingPapers/scriptsToMakeBams/tmp.list', WGS_INTERVAL, filters = WGS_FILTER)
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targets += targetsByStrategy(CallTarget, 'HiSeq.WGS.cleaned', BAM_ROOT + '/NA12878.HiSeq.WGS.bwa.cleaned.recal.bam', WGS_INTERVAL, filters = WGS_FILTER)
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# WE
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targets += targetsByStrategy(weTarget, 'GA2.WEx.cleaned', BAM_ROOT + '/NA12878.WEx.cleaned.recal.bam')
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targets += targetsByStrategy(weTarget, 'GA2.WEx.raw', '/seq/picard_aggregation/C308/NA12878/v3/NA12878.bam')
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#targets.append(weTarget('GA2.WEx.raw', '/seq/picard_aggregation/C308/NA12878/v3/NA12878.bam'))
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targets += targetsByStrategy(CallTarget, 'CG.WGS.raw', '/seq/complete_genomics/GS00106-DNA_E01-180_NA12878/SAM0/merge/NA12878.bam', WGS_INTERVAL, filters = WGS_FILTER)
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#targets += targetsByStrategy(CallTarget, 'CG.WGS.raw', '/seq/complete_genomics/GS00106-DNA_E01-180_NA12878/SAM0/merge/NA12878.bam', WGS_INTERVAL, filters = WGS_FILTER)
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# CG
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# todo -- fixme -- needs genome-wide bams on hg18
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@ -260,8 +260,8 @@ def callSNPs( myPipelineArgs, callTarget, ignore, lastJobs ):
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if callTarget.b36:
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outputVCF = appendExtension(outputVCF, "b36")
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print 'outputVCF', outputVCF
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ugArgs = '-T UnifiedGenotyper -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -I %s %s -varout %s %s' % (callTarget.getBam(), UG_ARGS, outputVCF, callTarget.getCallArgs())
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farmCmds = simpleGATKCommand( myPipelineArgs, 'UG', ugArgs, lastJobs )
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ugArgs = '-T UnifiedGenotyperV2 -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -I %s %s -o %s %s' % (callTarget.getBam(), UG_ARGS, outputVCF, callTarget.getCallArgs())
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farmCmds = simpleGATKCommand( myPipelineArgs, 'call.UG', ugArgs, lastJobs )
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if OPTIONS.splitByChr and not callTarget.hasInterval():
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farmCmds = splitGATKCommandByChr( myPipelineArgs, farmCmds[0], [outputVCF], [mergeVCFs] )
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return farmCmds, outputVCF
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@ -270,19 +270,20 @@ INDEL_MASK_SIZE = 10
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def getIndelCallFiles(callTarget):
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outputBed = appendExtension(callTarget.getVcf(), "indels.bed", False)
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outputVerbose = appendExtension(callTarget.getVcf(), "indels.verbose.txt", False)
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outputVCF = appendExtension(callTarget.getVcf(), "indels.vcf", False)
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outputMask = appendExtension(callTarget.getVcf(), "indels.%d.mask" % INDEL_MASK_SIZE, False)
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return outputBed, outputVerbose, outputMask
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return outputBed, outputVerbose, outputVCF, outputMask
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def callIndels( myPipelineArgs, callTarget, ignore, lastJobs ):
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outputBed, outputVerbose, outputMask = getIndelCallFiles(callTarget)
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IGV2_ARGS = '-T IndelGenotyperV2 -ws 500 -I %s -O %s -o %s --verbose -rf Platform454' % (callTarget.getBam(), outputBed, outputVerbose)
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farmCmds = simpleGATKCommand( myPipelineArgs, 'CallIndels', IGV2_ARGS, lastJobs )
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outputBed, outputVerbose, indelsVCF, outputMask = getIndelCallFiles(callTarget)
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IGV2_ARGS = '-T IndelGenotyperV2 -ws 500 -I %s -bed %s -verbose %s -o %s -rf Platform454' % (callTarget.getBam(), outputBed, outputVerbose, indelsVCF)
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farmCmds = simpleGATKCommand( myPipelineArgs, 'call.CallIndels', IGV2_ARGS, lastJobs )
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if OPTIONS.splitByChr and not callTarget.hasInterval():
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farmCmds = splitGATKCommandByChr( myPipelineArgs, farmCmds[0], [outputBed, outputVerbose], [mergeByCat, mergeByCat] )
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return farmCmds, None
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def createIndelMask( myPipelineArgs, callTarget, vcf, lastJobs ):
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outputBed, outputVerbose, outputMask = getIndelCallFiles(callTarget)
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outputBed, outputVerbose, outputVCF, outputMask = getIndelCallFiles(callTarget)
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cmd = 'python /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/python/makeIndelMask.py %s %d %s' % (outputBed, INDEL_MASK_SIZE, outputMask)
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jobs = [FarmJob(cmd, jobName = callTarget.name + '.' + 'makeIndelMask', dependencies = lastJobs)]
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return jobs, None
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@ -290,16 +291,17 @@ def createIndelMask( myPipelineArgs, callTarget, vcf, lastJobs ):
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def filterSNPs(myPipelineArgs, callTarget, vcf, lastJobs ):
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out = appendExtension(vcf, 'snpfiltered')
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filterString = ' '.join(map(lambda x: '--filterName %s --filterExpression "%s"' % (x[0], x[1]), callTarget.filters))
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return simpleGATKCommand( myPipelineArgs, 'filterSNPs', '-T VariantFiltration -B variant,VCF,%s -o %s --filterName LowQual --filterExpression "QUAL < 50.0" --clusterWindowSize 10 --filterName HARD_TO_VALIDATE --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" %s' % ( vcf, out, filterString ), lastJobs ), out
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return simpleGATKCommand( myPipelineArgs, 'call.filterSNPs', '-T VariantFiltration -B:variant,VCF %s -o %s --filterName LowQual --filterExpression "QUAL < 50.0" --clusterWindowSize 10 --filterName HARD_TO_VALIDATE --filterExpression "MQ0 >= 4 && ((MQ0 / (1.0 * DP)) > 0.1)" %s' % ( vcf, out, filterString ), lastJobs ), out
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def filterIndels(myPipelineArgs, callTarget, vcf, lastJobs ):
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out = appendExtension(vcf, 'indelfiltered')
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outputBed, outputVerbose, outputMask = getIndelCallFiles(callTarget)
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return simpleGATKCommand( myPipelineArgs, 'filterIndels', '-T VariantFiltration -B variant,VCF,%s -o %s --maskName Indel -B mask,Bed,%s' % ( vcf, out, outputMask ), lastJobs ), out
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outputBed, outputVerbose, outputVCF, outputMask = getIndelCallFiles(callTarget)
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return simpleGATKCommand( myPipelineArgs, 'call.filterIndels', '-T VariantFiltration -B:variant,VCF %s -o %s --maskName Indel -B:mask,Bed %s' % ( vcf, out, outputMask ), lastJobs ), out
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def VariantOptimizer( myPipelineArgs, callTarget, vcf, lastJobs ):
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if callTarget.optimize:
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clusterFile = appendExtension(vcf, 'optimized', False)
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clusterFile = appendExtension(vcf, 'optimized.clusters', False)
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tranchesFile = appendExtension(vcf, 'optimized.tranches', False)
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optOutVCF = appendExtension(vcf, 'optimized')
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out = appendExtension(vcf, 'optimized.cut')
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table = appendExtension(vcf, 'optimized.table', False)
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@ -314,24 +316,27 @@ def VariantOptimizer( myPipelineArgs, callTarget, vcf, lastJobs ):
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annotationsToOptimize = ['SB', 'HaplotypeScore', "QD", 'HRun']
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annotationsToOptimizeArg = ' '.join(map(lambda x: '-an ' + x, annotationsToOptimize)) # '' ['DP', 'SB', 'HaplotypeScore', 'MQ', "QD", 'HRun']
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#tranches = ' '.join(map( lambda x: '-tranche ' + str(x), [1, 5, 10]))
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tranches = ' '.join(map( lambda x: '-tranche ' + str(x), [0.1, 1, 2, 10]))
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tranches = ' '.join(map( lambda x: '-tranche ' + str(x), [0.1, 1, 10]))
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maxVariantsToShow = 2500
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#singletonFPRate = 0.2
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#hapmapVCF = '/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr.hg18_fwd.vcf'
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hapmapVCF = 'hapmap_analysis/sitesr27_nr.hg18_fwd.vcf'
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REGENERATE_VARIANT_CLUSTERS = True
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if ( REGENERATE_VARIANT_CLUSTERS ):
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jobs1 = simpleGATKCommand( myPipelineArgs, 'GenerateVariantClusters', '-T GenerateVariantClusters -qual %d -std 3.5 -mG %d -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B input,VCF,%s -clusterFile %s %s %s' % ( callTarget.minQual, callTarget.maxClusters, vcf, clusterFile, annotationsToOptimizeArg, IGNORE_FILTERS_CLUSTERING ), lastJobs )
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jobs1 = simpleGATKCommand( myPipelineArgs, 'call.GenerateVariantClusters', '-T GenerateVariantClusters -qual %d -std 3.5 -mG %d -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B:hapmap,vcf %s -B:input,VCF %s -clusterFile %s %s %s --NoByHapMapValidationStatus' % ( callTarget.minQual, callTarget.maxClusters, hapmapVCF, vcf, clusterFile, annotationsToOptimizeArg, IGNORE_FILTERS_CLUSTERING ), lastJobs )
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#jobs1 = simpleGATKCommand( myPipelineArgs, 'call.GenerateVariantClusters', '-T GenerateVariantClusters -qual %d -std 3.5 -mG %d -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B:input,VCF %s -clusterFile %s %s %s' % ( callTarget.minQual, callTarget.maxClusters, vcf, clusterFile, annotationsToOptimizeArg, IGNORE_FILTERS_CLUSTERING ), lastJobs )
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else:
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jobs1 = lastJobs
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jobs2 = simpleGATKCommand( myPipelineArgs, 'VariantRecalibrator', '-T VariantRecalibrator -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -qStep 0.01 -B input,VCF,%s -clusterFile %s -output %s --target_titv %f %s -resources ~/dev/GenomeAnalysisTK/trunk/R/ %s --known_prior %.2f' % ( vcf, clusterFile, os.path.splitext(optOutVCF)[0], callTarget.targetTiTv, IGNORE_FILTERS_SCORING, tranches, DBSNP_PRIOR ), jobs1 )
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jobs2 = simpleGATKCommand( myPipelineArgs, 'call.VariantRecalibrator', '-T VariantRecalibrator -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B:input,VCF %s -clusterFile %s -o %s --target_titv %f %s -resources ~/dev/GenomeAnalysisTK/trunk/R/ %s -priorDBSNP %.2f -tranchesFile %s' % ( vcf, clusterFile, optOutVCF, callTarget.targetTiTv, IGNORE_FILTERS_SCORING, tranches, DBSNP_PRIOR, tranchesFile ), jobs1 )
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cmd21 = 'python /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/python/vcf2table.py -f CHROM,POS,ID,AC,AF,AN,DB,' + ','.join(annotationsToOptimize) + ' ' + vcf + ' -o ' + table
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jobs21 = [FarmJob(cmd21, jobName = callTarget.name + '.' + 'VariantRecalibrationReport.vcf2table', dependencies = jobs2)]
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jobs21 = [FarmJob(cmd21, jobName = callTarget.name + '.call.' + 'VariantRecalibrationReport.vcf2table', dependencies = jobs2)]
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cmd22 = 'Rscript /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTK/trunk/R/VariantRecalibratorReport/VariantRecalibratorReport.R %s %s %s NA %d' % (clusterFile, clusterFile, table, maxVariantsToShow)
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jobs22 = [FarmJob(cmd22, jobName = callTarget.name + '.' + 'VariantRecalibrationReport.RScript', dependencies = jobs21)]
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jobs22 = [FarmJob(cmd22, jobName = callTarget.name + '.call.' + 'VariantRecalibrationReport.RScript', dependencies = jobs21)]
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jobs3 = simpleGATKCommand( myPipelineArgs, 'ApplyVariantCuts', '-T ApplyVariantCuts -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B input,VCF,%s -outputVCF %s --tranchesFile %s.dat.tranches --fdr_filter_level %f' % ( optOutVCF, out, clusterFile, callTarget.tranchToTake ), jobs2 )
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jobs3 = simpleGATKCommand( myPipelineArgs, 'call.ApplyVariantCuts', '-T ApplyVariantCuts -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B:input,VCF %s -o %s -tranchesFile %s --fdr_filter_level %f' % ( optOutVCF, out, tranchesFile, callTarget.tranchToTake ), jobs2 )
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return jobs1 + jobs2 + jobs21 + jobs22 + jobs3, out
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else:
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return [], vcf
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@ -346,25 +351,22 @@ def evalSNPs(myPipelineArgs, callTarget, vcf, lastJobs):
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evalRoot = OPTIONS.dir
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oldMemory = myPipelineArgs.memory
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myPipelineArgs.memory = '2g'
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myPipelineArgs.memory = '3g'
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def eval1(vcf, namePostfix = "", args = ""):
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out = os.path.join(OPTIONS.dir, os.path.basename(vcf) + namePostfix + ".ve2")
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#validation_bindings = "-B comp_p2_val,VCF," + VALIDATION_DIR + "/Validated/1kg_snp_validation/batch1-2.HG18.vcf -B comp_CG,VCF," + VALIDATION_DIR + "CG.vcf"
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maybeHiSeqBindings = ""
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hiSeqComp = os.path.join(OPTIONS.dir,"HiSeq.WGS.cleaned.ug.snpfiltered.indelfiltered.optimized.cut.vcf")
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omni = " -B compOmni,VCF,omni.na12878.hg18.vcf"
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omni = " -B:compOmni,VCF Omni.NA12878.hg18.vcf"
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if os.path.exists(hiSeqComp):
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maybeHiSeqBindings = "-B comp_HiSeq,VCF," + hiSeqComp + " "
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validation_bindings = maybeHiSeqBindings + "-B comp_p2_val,VCF,1kg_pilot2_snps.hg18.vcf -B comp_CG,VCF,/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/CG.hg18.vcf -B compTrio,VCF,CEU.trio.2010_03.genotypes.vcf -B compTrioNovel,VCF,CEU.trio.novels.2010_03.genotypes.vcf -B comp_hm3,VCF,/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/by_population/genotypes_CEU_phase3.2_consensus.hg18_fwd.vcf -B compDeNovo,VCF,/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/1kg_denovos/ceu_merged_validation_data_240610.annotated.hg18.vcf -B comp1KGCEU,VCF,YRI.low_coverage.2010_07.sites.vcf" + omni # not in hg18 space :-(
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maybeHiSeqBindings = "-B:comp_HiSeq,VCF " + hiSeqComp + " "
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validation_bindings = maybeHiSeqBindings + "-B:comp_p2_val,VCF 1kg_pilot2_snps.hg18.vcf -B:comp_CG,VCF /humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/NA12878/CG.hg18.vcf -B:compTrio,VCF CEU.trio.2010_03.genotypes.vcf -B:compTrioNovel,VCF CEU.trio.novels.2010_03.genotypes.vcf -B:comp_hm3,VCF /humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/by_population/genotypes_CEU_phase3.2_consensus.hg18_fwd.vcf " + omni # not in hg18 space :-(
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tranches = ""
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if vcf.find("optimized") != -1:
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args += " -tf " + appendExtension(vcf.replace(".cut", ""), 'dat.tranches', False)
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args += " -tf " + appendExtension(vcf.replace(".cut", ""), 'tranches', False)
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vcf = appendExtension(vcf.replace(".cut", ""), 'vcf', False)
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gatk_args = ("-T VariantEval -reportType Grep -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B eval,VCF,%s " + validation_bindings + " -sample NA12878 -o %s -E CompOverlap -E GenotypeConcordance -E TiTvVariantEvaluator -E CountVariants %s") % ( vcf, out, args )
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#gatk_args = ("-T VariantEval -reportType Grep -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -select \"hetCount == 1\" -selectName HET -select \"homVarCount == 1\" -selectName HOMVAR -B eval,VCF,%s " + validation_bindings + " -sample NA12878 -select \"QUAL <= 30.0\" -selectName LowQual -o %s -E CompOverlap -E GenotypeConcordance -E TiTvVariantEvaluator -E CountVariants %s") % ( vcf, out, args )
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gatk_args = ("-T VariantEval -reportType Grep -D /humgen/gsa-scr1/GATK_Data/dbsnp_129_hg18.rod -B:eval,VCF %s " + validation_bindings + " -sample NA12878 -o %s -E CompOverlap -E GenotypeConcordance -E TiTvVariantEvaluator -E CountVariants %s") % ( vcf, out, args )
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name = "EVAL_%s_%s" % (callTarget.name, namePostfix)
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# return FarmJob(cmd, jobName = "EVAL_%s_%s" % (callTarget.name, namePostfix), dependencies = lastJobs)
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return simpleGATKCommand( myPipelineArgs, name, gatk_args, lastJobs )[0]
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jobs = []
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