Reformatting and tweaks to the end-to-end pipeline
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4066 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
63ada20da5
commit
0028b884d8
|
|
@ -18,6 +18,9 @@ class fullCallingPipeline extends QScript {
|
|||
@Input(doc="trigger", shortName="trigger", required=false)
|
||||
var trigger: File = _
|
||||
|
||||
@Input(doc="compCEU",shortName="ceu",required=false)
|
||||
var comp1KGCEU: File = _
|
||||
|
||||
@Input(doc="refseqTable", shortName="refseqTable")
|
||||
var refseqTable: File = _
|
||||
|
||||
|
|
@ -36,156 +39,179 @@ class fullCallingPipeline extends QScript {
|
|||
@Input(doc="gatk jar")
|
||||
var gatkJar: File = _
|
||||
|
||||
trait CommandLineGATKArgs extends CommandLineGATK {
|
||||
this.intervals = qscript.intervals
|
||||
this.jarFile = qscript.gatkJar
|
||||
}
|
||||
@Input(doc="SNP cluster filter -- number SNPs",shortName="snpsInCluster",required=false)
|
||||
var snpsInCluster = 4
|
||||
|
||||
// ------------ SETUP THE PIPELINE ----------- //
|
||||
@Input(doc="SNP cluster filter -- window size",shortName="snpClusterWindow",required=false)
|
||||
var snpClusterWindow = 7
|
||||
|
||||
|
||||
|
||||
trait CommandLineGATKArgs extends CommandLineGATK {
|
||||
this.intervals = qscript.intervals
|
||||
this.jarFile = qscript.gatkJar
|
||||
}
|
||||
|
||||
// ------------ SETUP THE PIPELINE ----------- //
|
||||
|
||||
// todo -- the unclean and clean pipelines are the same, so the code can be condensed significantly
|
||||
|
||||
def script = {
|
||||
val projectBase: String = qscript.project
|
||||
val cleanedBase: String = projectBase + ".cleaned"
|
||||
val uncleanedBase: String = projectBase + ".uncleaned"
|
||||
// there are commands that use all the bam files
|
||||
// there are commands that use all the bam files
|
||||
var cleanBamFiles = List.empty[File]
|
||||
|
||||
for ( bam <- bamFiles ) {
|
||||
for ( bam <- bamFiles ) {
|
||||
|
||||
// put unclean bams in unclean genotypers
|
||||
// put unclean bams in unclean genotypers
|
||||
|
||||
// in advance, create the extension files
|
||||
// in advance, create the extension files
|
||||
|
||||
val indel_targets = swapExt(bam,"bam","realigner_targets.interval_list")
|
||||
val cleaned_bam = swapExt(bam,"bam","cleaned.bam") // note-- the scatter is in the definition itself
|
||||
val indel_targets = swapExt(bam,"bam","realigner_targets.interval_list")
|
||||
val cleaned_bam = swapExt(bam,"bam","cleaned.bam") // note-- the scatter is in the definition itself
|
||||
|
||||
// create the cleaning commands
|
||||
// create the cleaning commands
|
||||
|
||||
val targetCreator = new RealignerTargetCreator with CommandLineGATKArgs
|
||||
targetCreator.input_file :+= bam
|
||||
targetCreator.out = indel_targets
|
||||
val targetCreator = new RealignerTargetCreator with CommandLineGATKArgs
|
||||
targetCreator.input_file :+= bam
|
||||
targetCreator.out = indel_targets
|
||||
|
||||
val realigner = new IndelRealigner with CommandLineGATKArgs
|
||||
realigner.input_file = targetCreator.input_file
|
||||
realigner.intervals = qscript.contigIntervals
|
||||
//realigner.targetIntervals = targetCreator.out
|
||||
realigner.targetIntervals = targetCreator.out.getAbsolutePath
|
||||
realigner.scatterCount = qscript.numContigs
|
||||
realigner.out = cleaned_bam
|
||||
realigner.scatterClass = classOf[ContigScatterFunction]
|
||||
realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
|
||||
realigner.jobQueue = "long"
|
||||
val realigner = new IndelRealigner with CommandLineGATKArgs
|
||||
realigner.input_file = targetCreator.input_file
|
||||
realigner.intervals = qscript.contigIntervals
|
||||
realigner.targetIntervals = targetCreator.out.getAbsolutePath
|
||||
realigner.scatterCount = qscript.numContigs
|
||||
realigner.out = cleaned_bam
|
||||
realigner.scatterClass = classOf[ContigScatterFunction]
|
||||
realigner.setupGatherFunction = { case (f: BamGatherFunction, _) => f.jarFile = qscript.picardFixMatesJar }
|
||||
realigner.jobQueue = "week"
|
||||
|
||||
// put clean bams in clean genotypers
|
||||
// put clean bams in clean genotypers
|
||||
|
||||
cleanBamFiles :+= realigner.out
|
||||
cleanBamFiles :+= realigner.out
|
||||
|
||||
add(targetCreator,realigner)
|
||||
}
|
||||
add(targetCreator,realigner)
|
||||
}
|
||||
|
||||
// actually make calls
|
||||
endToEnd(uncleanedBase,bamFiles)
|
||||
endToEnd(cleanedBase,cleanBamFiles)
|
||||
}
|
||||
|
||||
def endToEnd(base: String, bamFiles: List[File]) = {
|
||||
def endToEnd(base: String, bamFiles: List[File]) = {
|
||||
|
||||
// step through the un-indel-cleaned graph:
|
||||
// 1a. call snps and indels
|
||||
val snps = new UnifiedGenotyper with CommandLineGATKArgs
|
||||
snps.input_file = bamFiles
|
||||
snps.group :+= "Standard"
|
||||
snps.annotation :+= "MyHamplotypeScore"
|
||||
snps.variants_out = new File(base+".vcf")
|
||||
snps.standard_min_confidence_threshold_for_emitting = Some(10)
|
||||
snps.min_mapping_quality_score = Some(20)
|
||||
snps.min_base_quality_score = Some(20)
|
||||
snps.downsampling_type = Some(DownsampleType.EXPERIMENTAL_BY_SAMPLE)
|
||||
snps.downsample_to_coverage = Some(200)
|
||||
// todo -- add input for comps, triggers, etc
|
||||
if (qscript.trigger != null) {
|
||||
snps.trigger_min_confidence_threshold_for_calling = Some(30)
|
||||
snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger)
|
||||
}
|
||||
// todo -- hack -- get this from the command line, or properties
|
||||
snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/CEU.low_coverage.2010_07.sites.hg18.vcf.gz") )
|
||||
// step through the un-indel-cleaned graph:
|
||||
// 1a. call snps and indels
|
||||
val snps = new UnifiedGenotyper with CommandLineGATKArgs
|
||||
snps.input_file = bamFiles
|
||||
snps.group :+= "Standard"
|
||||
snps.variants_out = new File(base+".vcf")
|
||||
snps.standard_min_confidence_threshold_for_emitting = Some(10)
|
||||
snps.min_mapping_quality_score = Some(20)
|
||||
snps.min_base_quality_score = Some(20)
|
||||
snps.downsampling_type = Some(DownsampleType.EXPERIMENTAL_BY_SAMPLE)
|
||||
snps.downsample_to_coverage = Some(200)
|
||||
snps.annotation :+= "QualByDepthV2"
|
||||
|
||||
if (qscript.trigger != null) {
|
||||
snps.trigger_min_confidence_threshold_for_calling = Some(30)
|
||||
snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger)
|
||||
// TODO: triggers need to get a name for comp-ing them if not dbSNP?
|
||||
snps.rodBind :+= RodBind( "compTrigger", "VCF", qscript.trigger )
|
||||
}
|
||||
|
||||
// todo -- add generalize comp inputs
|
||||
if ( qscript.comp1KGCEU != null ) {
|
||||
snps.rodBind :+= RodBind( "comp1KG_CEU", "VCF", qscript.comp1KGCEU )
|
||||
}
|
||||
|
||||
snps.scatterCount = 50
|
||||
|
||||
|
||||
// TODO: what is the 1KG_ALL track? -- same as trigger -- just makes sure the field is propagated :: chartl
|
||||
snps.rodBind :+= RodBind( "comp1KG_ALL", "VCF", qscript.trigger )
|
||||
val indels = new UnifiedGenotyper with CommandLineGATKArgs
|
||||
indels.input_file = bamFiles
|
||||
indels.downsampling_type = Some(DownsampleType.EXPERIMENTAL_BY_SAMPLE)
|
||||
indels.downsample_to_coverage = Some(200)
|
||||
indels.variants_out = new File(base+".indels.vcf")
|
||||
indels.genotype_model = Some(Model.INDELS)
|
||||
indels.scatterCount = 50
|
||||
|
||||
|
||||
snps.scatterCount = 100
|
||||
val indels = new UnifiedGenotyper with CommandLineGATKArgs
|
||||
indels.input_file = bamFiles
|
||||
indels.variants_out = new File(base+".indels.vcf")
|
||||
indels.genotype_model = Some(Model.INDELS)
|
||||
indels.scatterCount = 100
|
||||
// todo -- add inputs for the indel genotyper
|
||||
// 1b. genomically annotate SNPs -- slow, but scatter it
|
||||
val annotated = new GenomicAnnotator with CommandLineGATKArgs
|
||||
annotated.rodBind :+= RodBind("variant", "VCF", snps.variants_out)
|
||||
annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
|
||||
annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
|
||||
annotated.vcfOutput = swapExt(snps.variants_out,".vcf",".annotated.vcf")
|
||||
annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
|
||||
annotated.rodToIntervalTrackName = "variant"
|
||||
annotated.scatterCount = 100
|
||||
// 2.a filter on cluster and near indels
|
||||
val masker = new VariantFiltration with CommandLineGATKArgs
|
||||
masker.rodBind :+= RodBind("variant", "VCF", annotated.vcfOutput)
|
||||
masker.rodBind :+= RodBind("mask", "VCF", indels.variants_out)
|
||||
masker.maskName = "NearIndel"
|
||||
masker.clusterWindowSize = Some(20)
|
||||
masker.clusterSize = Some(7)
|
||||
masker.out = swapExt(annotated.vcfOutput,".vcf",".indel.masked.vcf")
|
||||
// todo -- snp cluster args?
|
||||
// 2.b hand filter with standard filter
|
||||
val handFilter = new VariantFiltration with CommandLineGATKArgs
|
||||
handFilter.rodBind :+= RodBind("variant", "VCF", annotated.vcfOutput)
|
||||
handFilter.rodBind :+= RodBind("mask", "VCF", indels.variants_out)
|
||||
handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
|
||||
handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
|
||||
handFilter.out = swapExt(annotated.vcfOutput,".vcf",".handfiltered.vcf")
|
||||
// 3.i generate gaussian clusters on the masked vcf
|
||||
val clusters = new GenerateVariantClusters with CommandLineGATKArgs
|
||||
clusters.rodBind :+= RodBind("input", "VCF", masker.out)
|
||||
//clusters.clusterFile = swapExt(snps.variants_out,".vcf",".cluster")
|
||||
val clusters_clusterFile = swapExt(snps.variants_out,".vcf",".cluster")
|
||||
clusters.clusterFile = clusters_clusterFile.getAbsolutePath
|
||||
clusters.memoryLimit = Some(8)
|
||||
clusters.jobQueue = "hugemem"
|
||||
// todo -- args for annotations?
|
||||
// todo -- args for resources (properties file)
|
||||
clusters.use_annotation ++= List("QD", "SB", "MyHaplotypeScore", "HRun")
|
||||
clusters.path_to_resources = "/humgen/gsa-scr1/chartl/sting/R"
|
||||
// 3.ii apply gaussian clusters to the masked vcf
|
||||
val recalibrate = new VariantRecalibrator with CommandLineGATKArgs
|
||||
recalibrate.clusterFile = clusters.clusterFile
|
||||
recalibrate.rodBind :+= RodBind("input", "VCF", masker.out)
|
||||
recalibrate.out = swapExt(masker.out,".vcf",".optimized.vcf")
|
||||
// todo -- inputs for Ti/Tv expectation and other things
|
||||
recalibrate.target_titv = Some(2.1)
|
||||
// 3.iii apply variant cuts to the clusters
|
||||
val cut = new ApplyVariantCuts with CommandLineGATKArgs
|
||||
cut.rodBind :+= RodBind("input", "VCF", recalibrate.out)
|
||||
//cut.outputVCFFile = swapExt(recalibrate.out,".vcf",".tranched.vcf")
|
||||
//cut.tranchesFile = swapExt(recalibrate.out,".vcf",".tranch")
|
||||
val cut_outputVCFFile = swapExt(recalibrate.out,".vcf",".tranched.vcf")
|
||||
val cut_tranchesFile = swapExt(recalibrate.out,".vcf",".tranch")
|
||||
cut.outputVCFFile = cut_outputVCFFile.getAbsolutePath
|
||||
cut.tranchesFile = cut_tranchesFile.getAbsolutePath
|
||||
// todo -- fdr inputs, etc
|
||||
cut.fdr_filter_level = Some(10)
|
||||
// 4. Variant eval the cut and the hand-filtered vcf files
|
||||
val eval = new VariantEval with CommandLineGATKArgs
|
||||
eval.rodBind :+= RodBind("evalOptimized", "VCF", cut_outputVCFFile)
|
||||
eval.rodBind :+= RodBind("evalHandFiltered", "VCF", handFilter.out)
|
||||
// todo -- make comp tracks command-line arguments or properties
|
||||
eval.evalModule ++= List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator")
|
||||
eval.out = new File(base+".eval")
|
||||
// 1b. genomically annotate SNPs -- slow, but scatter it
|
||||
val annotated = new GenomicAnnotator with CommandLineGATKArgs
|
||||
annotated.rodBind :+= RodBind("variant", "VCF", snps.variants_out)
|
||||
annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
|
||||
annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
|
||||
annotated.vcfOutput = swapExt(snps.variants_out,".vcf",".annotated.vcf")
|
||||
annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
|
||||
annotated.rodToIntervalTrackName = "variant"
|
||||
annotated.scatterCount = 100
|
||||
|
||||
add(snps,indels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
|
||||
}
|
||||
|
||||
// 2.a filter on cluster and near indels
|
||||
val masker = new VariantFiltration with CommandLineGATKArgs
|
||||
masker.rodBind :+= RodBind("variant", "VCF", annotated.vcfOutput)
|
||||
masker.rodBind :+= RodBind("mask", "VCF", indels.variants_out)
|
||||
masker.maskName = "NearIndel"
|
||||
masker.clusterWindowSize = Some(qscript.snpClusterWindow)
|
||||
masker.clusterSize = Some(qscript.snpsInCluster)
|
||||
masker.out = swapExt(annotated.vcfOutput,".vcf",".indel.masked.vcf")
|
||||
|
||||
|
||||
// 2.b hand filter with standard filter
|
||||
val handFilter = new VariantFiltration with CommandLineGATKArgs
|
||||
handFilter.rodBind :+= RodBind("variant", "VCF", annotated.vcfOutput)
|
||||
handFilter.rodBind :+= RodBind("mask", "VCF", indels.variants_out)
|
||||
handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
|
||||
handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
|
||||
handFilter.out = swapExt(annotated.vcfOutput,".vcf",".handfiltered.vcf")
|
||||
|
||||
|
||||
// 3.i generate gaussian clusters on the masked vcf
|
||||
// todo -- args for annotations?
|
||||
// todo -- args for resources (properties file)
|
||||
val clusters = new GenerateVariantClusters with CommandLineGATKArgs
|
||||
clusters.rodBind :+= RodBind("input", "VCF", masker.out)
|
||||
val clusters_clusterFile = swapExt(snps.variants_out,".vcf",".cluster")
|
||||
clusters.clusterFile = clusters_clusterFile.getAbsolutePath
|
||||
clusters.memoryLimit = Some(8)
|
||||
clusters.jobQueue = "hugemem"
|
||||
|
||||
clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
|
||||
clusters.path_to_resources = "/humgen/gsa-scr1/chartl/sting/R"
|
||||
|
||||
|
||||
// 3.ii apply gaussian clusters to the masked vcf
|
||||
val recalibrate = new VariantRecalibrator with CommandLineGATKArgs
|
||||
recalibrate.clusterFile = clusters.clusterFile
|
||||
recalibrate.rodBind :+= RodBind("input", "VCF", masker.out)
|
||||
recalibrate.out = swapExt(masker.out,".vcf",".optimized.vcf")
|
||||
// todo -- inputs for Ti/Tv expectation and other things -- command line
|
||||
recalibrate.target_titv = Some(2.1)
|
||||
|
||||
|
||||
// 3.iii apply variant cuts to the clusters
|
||||
val cut = new ApplyVariantCuts with CommandLineGATKArgs
|
||||
cut.rodBind :+= RodBind("input", "VCF", recalibrate.out)
|
||||
//cut.outputVCFFile = swapExt(recalibrate.out,".vcf",".tranched.vcf")
|
||||
//cut.tranchesFile = swapExt(recalibrate.out,".vcf",".tranch")
|
||||
val cut_outputVCFFile = swapExt(recalibrate.out,".vcf",".tranched.vcf")
|
||||
val cut_tranchesFile = swapExt(recalibrate.out,".vcf",".tranch")
|
||||
cut.outputVCFFile = cut_outputVCFFile.getAbsolutePath
|
||||
cut.tranchesFile = cut_tranchesFile.getAbsolutePath
|
||||
// todo -- fdr inputs, etc
|
||||
cut.fdr_filter_level = Some(10)
|
||||
|
||||
|
||||
// 4. Variant eval the cut and the hand-filtered vcf files
|
||||
val eval = new VariantEval with CommandLineGATKArgs
|
||||
eval.rodBind :+= RodBind("evalOptimized", "VCF", cut_outputVCFFile)
|
||||
eval.rodBind :+= RodBind("evalHandFiltered", "VCF", handFilter.out)
|
||||
eval.evalModule ++= List("CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator")
|
||||
eval.out = new File(base+".eval")
|
||||
|
||||
add(snps,indels,annotated,masker,handFilter,clusters,recalibrate,cut,eval)
|
||||
}
|
||||
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue