def mapEachInterval(self, workflow=None, intervalData=None, chromosome=None, \
VCFJobData=None, passingData=None,
mapEachChromosomeData=None, transferOutput=False, \
**keywords):
"""
2013.04.30
"""
if workflow is None:
workflow = self
returnData = PassingData(no_of_jobs = 0)
returnData.jobDataLs = []
topOutputDirJob = passingData.topOutputDirJob
intervalFileBasenamePrefix = passingData.intervalFileBasenamePrefix
span = passingData.span
noOfIndividuals= passingData.noOfIndividuals
SNPVCFFile = VCFJobData.file
SNPVCFJobLs = VCFJobData.jobLs
"""
### 2013.06.19 intervalData does not exsit for input that is entirely composed of VCF files (SplitVCFFile job does not return intervals)
if intervalData.file:
mpileupInterval = intervalData.interval
bcftoolsInterval = intervalData.file
else:
mpileupInterval = intervalData.interval
bcftoolsInterval = intervalData.interval
intervalFileBasenameSignature = intervalData.intervalFileBasenameSignature
overlapInterval = intervalData.overlapInterval
overlapFileBasenameSignature = intervalData.overlapIntervalFnameSignature
span = intervalData.span
"""
if chromosome is None:
chromosome = getattr(passingData, 'chromosome', None)
#noOfIndividuals
realInputVolume = noOfIndividuals * span
baseInputVolume = 600*2000 #600 individuals at 2000 sites
walltime = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=10000).value
#splitVCFJob = passingData.mapEachVCFData.splitVCFJob
#### Part 1 generate high-quality reference panel through Beagle on high-coverage individuals
# extractRefPanelSampleIDJob outputs sample IDs with replicate tags
# select the high-coverage members
outputVCF = File(os.path.join(self.highCoveragePanelDirJob.output, \
'%s.minCoverageForRefPanel%s.vcf'%(intervalFileBasenamePrefix, self.minCoverageForRefPanel)))
#selectVariants would re-generate AC, AF so that TrioCaller could read it.
#samtools uses 'AC1' instead of AC, 'AF1' instead of AF.
selectHighCoverageSampleJob = self.addSelectVariantsJob(SelectVariantsJava=self.SelectVariantsJava, \
inputF=VCFJobData.file, outputF=outputVCF, \
refFastaFList=self.registerReferenceData.refFastaFList, sampleIDKeepFile=self.extractRefPanelSampleIDJob.output,\
parentJobLs=[self.highCoveragePanelDirJob, self.extractRefPanelSampleIDJob] + VCFJobData.jobLs, \
extraDependentInputLs=[VCFJobData.tbi_F], transferOutput=False, \
extraArguments=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=9000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value)
# run Beagle
outputFnamePrefix = os.path.join(self.highCoveragePanelDirJob.folder, "%s.minCoverage%s.beagled"%\
(intervalFileBasenamePrefix, self.minCoverageForRefPanel))
beagleOnHighCoverageJob = self.addBeagle4Job(executable=self.BeagleOnHCMOnkeys, \
inputFile=selectHighCoverageSampleJob.output, refPanelFile=None,\
pedFile = self.outputPedigreeOfHghCoverageSamplesJob.output,\
outputFnamePrefix=outputFnamePrefix, \
burninIterations=7, phaseIterations=10, \
noOfSamplingHaplotypesPerSample=4,\
parentJobLs=[self.highCoveragePanelDirJob, selectHighCoverageSampleJob, self.outputPedigreeOfHghCoverageSamplesJob], \
transferOutput=False, \
extraArguments=None, extraArgumentList=None,\
extraOutputLs=None, extraDependentInputLs=None, \
no_of_cpus=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=13000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value)
#index .vcf.gz, output of beagle, without index, GATK can't work on gzipped vcf
tabixIndexFile = File('%s.tbi'%(beagleOnHighCoverageJob.output.name))
tabixOnHighCoverageVCFJob = self.addGenericJob(executable=self.tabix, \
inputFile=beagleOnHighCoverageJob.output, inputArgumentOption="",\
outputFile=None, outputArgumentOption="-o", \
extraDependentInputLs=None, \
extraOutputLs=[tabixIndexFile], transferOutput=False, frontArgumentList=["-p vcf"], \
extraArguments=None, \
extraArgumentList=[], \
parentJobLs=[beagleOnHighCoverageJob, self.highCoveragePanelDirJob],\
no_of_cpus=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=2000, maxJobPropertyValue=5000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=600).value)
# select the high-coverage members
outputVCF = File(os.path.join(self.highCoveragePanelDirJob.output, \
'%s.minCoverage%s.maxPairwiseKinship%s.refPanel.beagled.vcf'%\
(intervalFileBasenamePrefix, self.minCoverageForRefPanel, self.maxPairwiseKinship)))
#selectVariants would re-generate AC, AF so that TrioCaller could read it.
#samtools uses 'AC1' instead of AC, 'AF1' instead of AF.
selectDistantMembersVariantsJob = self.addSelectVariantsJob(SelectVariantsJava=self.SelectVariantsJava, \
inputF=beagleOnHighCoverageJob.output, outputF=outputVCF, \
refFastaFList=self.registerReferenceData.refFastaFList, \
sampleIDKeepFile=self.selectDistantMembersFromGenotypeFileJob.output,\
parentJobLs=[self.highCoveragePanelDirJob, beagleOnHighCoverageJob, self.selectDistantMembersFromGenotypeFileJob,\
tabixOnHighCoverageVCFJob], \
extraDependentInputLs=[tabixOnHighCoverageVCFJob.output], transferOutput=False, \
extraArguments=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=7000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value)
##### Part 2 run Beagle on everyone with reference panel
# run Beagle
#refPanelFile=selectDistantMembersVariantsJob.output,\
outputFnamePrefix = os.path.join(self.mapDirJob.folder, '%s.beagled'%(intervalFileBasenamePrefix))
beagleJob = self.addBeagle4Job(executable=self.BeagleJava, \
inputFile=VCFJobData.file, refPanelFile=None,\
pedFile=self.outputPedigreeJob.output,\
outputFnamePrefix=outputFnamePrefix, \
burninIterations=7, phaseIterations=10, \
noOfSamplingHaplotypesPerSample=4, duoscale=2, trioscale=2, \
extraArguments=None, extraArgumentList=None,\
parentJobLs=[self.mapDirJob, \
self.outputPedigreeJob] + VCFJobData.jobLs, \
transferOutput=False, no_of_cpus=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=13000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value,\
)
returnData.beagleJob = beagleJob
#index .vcf.gz, output of beagle, without index, GATK can't work on gzipped vcf
tabixIndexFile = File('%s.tbi'%(beagleJob.output.name))
tabixJob = self.addGenericJob(executable=self.tabix, \
inputFile=beagleJob.output, inputArgumentOption="",\
outputFile=None, outputArgumentOption="-o", \
extraDependentInputLs=None, \
extraOutputLs=[tabixIndexFile], transferOutput=False, frontArgumentList=["-p vcf"], \
extraArguments=None, \
extraArgumentList=[], \
parentJobLs=[beagleJob, self.mapDirJob],\
no_of_cpus=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=2000, maxJobPropertyValue=4000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=600).value)
#borrow PL to from pre-Beagle VCF to genotype
outputFile = File(os.path.join(self.mapDirJob.folder, '%s.beagled.withPL.vcf'%(intervalFileBasenamePrefix)))
combineBeagleAndPreBeagleVariantsJob = self.addGATKJob(executable=self.CombineBeagleAndPreBeagleVariantsJava, \
GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
GATKAnalysisType="CombineBeagleAndPreBeagleVariants",\
inputFile=None, inputArgumentOption=None, \
refFastaFList=self.registerReferenceData.refFastaFList, \
inputFileList=None, argumentForEachFileInInputFileList="--variant",\
interval=None, outputFile=outputFile, outputArgumentOption="--out", \
frontArgumentList=None, extraArguments=None, \
extraArgumentList=["--variant:first", beagleJob.output, "--variant:second", VCFJobData.file, \
"-genotypeMergeOptions PRIORITIZE", "-priority first,second"], \
extraOutputLs=None, \
extraDependentInputLs=[beagleJob.output, VCFJobData.file] + tabixJob.outputLs, \
parentJobLs=[beagleJob, tabixJob]+ VCFJobData.jobLs, transferOutput=False, \
no_of_cpus=None, \
key2ObjectForJob=None,\
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=2000, maxJobPropertyValue=4000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=600).value)
#do not use "--variant:beagle" to name your vcf file as GATK would think it's in Beagle format
#TrioCaller
# 2013.06.11 replicate individuals who appear in more than 1 families
round1_IndividualsReplicatedVCF = File( os.path.join(self.mapDirJob.folder, \
'%s.replicate.vcf'%(intervalFileBasenamePrefix)))
replicateVCFGenotypeColumnsJob = self.addReplicateVCFGenotypeColumnsJob(\
executable=self.ReplicateVCFGenotypeColumns, \
inputF=combineBeagleAndPreBeagleVariantsJob.output, \
sampleID2FamilyCountF=self.outputReplicatePedigreeJob.sampleID2FamilyCountF, \
outputF=round1_IndividualsReplicatedVCF, \
replicateIndividualTag=self.replicateIndividualTag,\
parentJobLs=[self.outputReplicatePedigreeJob, self.mapDirJob, combineBeagleAndPreBeagleVariantsJob], \
extraDependentInputLs=None, \
transferOutput=False, \
extraArguments=None, \
job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=9000).value, \
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value,\
)
refineGenotypeOutputF = File(os.path.join(self.mapDirJob.folder, \
'%s.trioCaller.vcf'%(intervalFileBasenamePrefix)))
refineGenotypeJob = self.addTrioCallerJob(trioCallerWrapper=self.trioCallerWrapper, \
trioCallerPath=self.trioCallerPath, \
inputVCF=replicateVCFGenotypeColumnsJob.output,\
pedFile=self.outputReplicatePedigreeJob.output, outputVCF=refineGenotypeOutputF, \
inputPhased=True,\
parentJobLs=[self.mapDirJob, replicateVCFGenotypeColumnsJob, self.outputReplicatePedigreeJob], \
extraDependentInputLs=[], transferOutput=False, \
extraArguments=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=9000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value) #1.2G memory for 12K loci
returnData.refineGenotypeJob = refineGenotypeJob
"""
2013.07.10 the TrioCaller VCF has some info tags that are not described in VCF header
"""
outputFile = File(os.path.join(self.mapDirJob.folder, \
'%s.extraInfoDesc.vcf'%(intervalFileBasenamePrefix)))
addInfoDescJob = self.addGenericJob(executable=self.AddMissingInfoDescriptionToVCFHeader, \
inputFile=refineGenotypeJob.output, \
inputArgumentOption="-i", \
outputFile=outputFile, outputArgumentOption="-o", \
parentJobLs=[self.mapDirJob, refineGenotypeJob], \
extraDependentInputLs=None, extraOutputLs=None, \
frontArgumentList=None, extraArguments=None, extraArgumentList=None, \
transferOutput=False, sshDBTunnel=None, \
key2ObjectForJob=None, objectWithDBArguments=None, \
no_of_cpus=None,
job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=2000, \
minJobPropertyValue=1000, maxJobPropertyValue=3000).value, \
walltime=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=500).value,\
max_walltime=None)
# a CheckGenotypeConcordanceAmongReplicates.py job
trioCallerReplicateConcordanceFile = File(os.path.join(self.statDirJob.folder, \
'%s.trioCaller.concordance.tsv'%(intervalFileBasenamePrefix)))
returnData.trioCallerReplicateConcordanceJob = self.addGATKJob(executable=self.CalculateConcordanceJava, \
GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
GATKAnalysisType="CalculateConcordanceAmongReplicates",\
inputFile=refineGenotypeJob.output, inputArgumentOption="--variant", \
refFastaFList=self.registerReferenceData.refFastaFList, \
interval=None, \
outputFile=trioCallerReplicateConcordanceFile, outputArgumentOption="--concordanceStatFname",\
frontArgumentList=None, extraArguments="--replicateIndividualTag %s"%(self.replicateIndividualTag), \
extraArgumentList=None, extraOutputLs=None, \
parentJobLs=[self.statDirJob, refineGenotypeJob], \
transferOutput=False, \
no_of_cpus=None, \
job_max_memory=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=6000, \
minJobPropertyValue=9000, maxJobPropertyValue=16000).value, \
walltime=self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value)
#2013.06.14
#merge replicates to generate consensus call
# (not haplotype-based, as different recombination points across replicate haplotypes make it non-trivial )
mergeReplicateOutputF = File(os.path.join(self.mapDirJob.folder, \
'%s.replicatesMerged.vcf'%(intervalFileBasenamePrefix)))
returnData.mergeVCFReplicateColumnsJob = self.addMergeVCFReplicateGenotypeColumnsJob(\
executable=self.MergeVCFReplicateHaplotypesJava,\
GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
inputF=addInfoDescJob.output, outputF=mergeReplicateOutputF, \
replicateIndividualTag=self.replicateIndividualTag, \
refFastaFList=self.registerReferenceData.refFastaFList, \
parentJobLs=[self.mapDirJob, addInfoDescJob], \
extraDependentInputLs=[], transferOutput=False, \
extraArguments=None, \
analysis_type='MergeVCFReplicateGenotypeColumns',\
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=5000, maxJobPropertyValue=9000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value)
return returnData
def addRefineGenotypeJobsViaBeagle(self, inputFile=None, vcfBaseFname=None, outputDirJob=None, statDirJob=None, \
refFastaFList=None, intervalData=None,\
baseInputVolume=450*2000000, realInputVolume=None,\
parentJobLs=None, \
transferOutput=False, \
no_of_cpus=None, job_max_memory=2000, walltime=180, \
max_walltime=None, **keywords):
returnData = PassingData()
if not hasattr(self, "outputPedigreeJob"):
#output pedigree, with no replicating certain individuals, no trio/duo splitting
#plink format
#for Beagle to read in
pedigreeFileFormat = 4
inputFileBasenamePrefix = utils.getFileBasenamePrefixFromPath(inputFile.name)
pedFile = File(os.path.join(outputDirJob.output, 'pedigree.%s.format%s.txt'%\
(inputFileBasenamePrefix, pedigreeFileFormat)))
#sampleID2FamilyCountF = File(os.path.join(self.auxDirJob.output, 'pedigree.sampleID2FamilyCount.%s.format%s.txt'%\
# (inputFileBasenamePrefix, pedigreeFileFormat)))
self.outputPedigreeJob = self.addOutputVRCPedigreeInTFAMGivenOrderFromFileJob(executable=self.OutputVRCPedigreeInTFAMGivenOrderFromFile, \
inputFile=inputFile, outputFile=pedFile, \
sampleID2FamilyCountF=None,\
polymuttDatFile = None,\
outputFileFormat=pedigreeFileFormat, \
replicateIndividualTag=self.replicateIndividualTag,\
treatEveryOneIndependent=self.treatEveryOneIndependent,\
parentJobLs=parentJobLs + [outputDirJob], \
extraDependentInputLs=None, transferOutput=True, \
extraArguments=None, job_max_memory=2000, sshDBTunnel=self.needSSHDBTunnel)
##### Part 2 run Beagle on everyone with reference panel
# run Beagle
#refPanelFile=selectDistantMembersVariantsJob.output,\
outputFnamePrefix = os.path.join(outputDirJob.folder, '%s.beagled'%(vcfBaseFname))
beagleJob = self.addBeagle4Job(executable=self.BeagleJava, \
inputFile=inputFile, refPanelFile=None,\
pedFile=self.outputPedigreeJob.output,\
outputFnamePrefix=outputFnamePrefix, \
burninIterations=7, phaseIterations=10, \
noOfSamplingHaplotypesPerSample=4, duoscale=2, trioscale=2, \
extraArguments=None, extraArgumentList=None,\
parentJobLs=[outputDirJob, \
self.outputPedigreeJob] + parentJobLs, \
transferOutput=False, no_of_cpus=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=4000, maxJobPropertyValue=13000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=1200).value,\
)
returnData.beagleJob = beagleJob
#index .vcf.gz, output of beagle, without index, GATK can't work on gzipped vcf
tabixIndexFile = File('%s.tbi'%(beagleJob.output.name))
tabixJob = self.addGenericJob(executable=self.tabix, \
inputFile=beagleJob.output, inputArgumentOption="",\
outputFile=None, outputArgumentOption="-o", \
extraDependentInputLs=None, \
extraOutputLs=[beagleJob.output, tabixIndexFile], transferOutput=False, \
frontArgumentList=["-p vcf"], \
extraArguments=None, \
extraArgumentList=None, \
parentJobLs=[beagleJob, outputDirJob],\
no_of_cpus=None, \
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=2000, maxJobPropertyValue=4000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=180).value)
#borrow PL to from pre-Beagle VCF to genotype
outputFile = File(os.path.join(outputDirJob.folder, '%s.beagled.withPL.vcf'%(vcfBaseFname)))
combineBeagleAndPreBeagleVariantsJob = self.addGATKJob(executable=self.CombineBeagleAndPreBeagleVariantsJava, \
GenomeAnalysisTKJar=self.GenomeAnalysisTKJar, \
GATKAnalysisType="CombineBeagleAndPreBeagleVariants",\
inputFile=None, inputArgumentOption=None, \
refFastaFList=refFastaFList, \
inputFileList=None, argumentForEachFileInInputFileList="--variant",\
interval=None, outputFile=outputFile, outputArgumentOption="--out", \
frontArgumentList=None, extraArguments=None, \
extraArgumentList=["--variant:first", beagleJob.output, "--variant:second", inputFile, \
"-genotypeMergeOptions PRIORITIZE", "-priority first,second"], \
extraOutputLs=None, \
extraDependentInputLs=[inputFile] + tabixJob.outputLs, \
parentJobLs=[beagleJob, tabixJob]+ parentJobLs, transferOutput=False, \
no_of_cpus=None, \
key2ObjectForJob=None,\
job_max_memory = self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=4000, \
minJobPropertyValue=2000, maxJobPropertyValue=4000).value,\
walltime= self.scaleJobWalltimeOrMemoryBasedOnInput(realInputVolume=realInputVolume, \
baseInputVolume=baseInputVolume, baseJobPropertyValue=60, \
minJobPropertyValue=60, maxJobPropertyValue=600).value)
#do not use "--variant:beagle" to name your vcf file as GATK would think it's in Beagle format
returnData.refineGenotypeJob = combineBeagleAndPreBeagleVariantsJob #the final gentoype job
returnData.refineGenotypeJob.intervalData = intervalData #attached so that it could be used by downstream jobs
return returnData
