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Taking out recalibrating for now, since having these files is confusing people and we've not gone to dbsnp 132 yet so cluster generation's broken with these command lines. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4786 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2010-12-03 22:12:09 +00:00
parent b12cec4302
commit bdc7516168
1 changed files with 31 additions and 31 deletions
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62
scala/qscript/fullCallingPipeline.q
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@ -205,7 +205,7 @@ class fullCallingPipeline extends QScript {
snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out") snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out")
snps.analysisName = base+"_SNP_calls" snps.analysisName = base+"_SNP_calls"
snps.input_file = bamFiles snps.input_file = bamFiles
snps.annotation ++= List("AlleleBalance") //snps.annotation ++= List("AlleleBalance")
snps.input_file = bamFiles snps.input_file = bamFiles
snps.group :+= "Standard" snps.group :+= "Standard"
snps.out = new File("SnpCalls", base+".vcf") snps.out = new File("SnpCalls", base+".vcf")
@ -215,7 +215,7 @@ class fullCallingPipeline extends QScript {
snps.downsample_to_coverage = Some(qscript.downsampling_coverage) snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
//snps.annotation :+= "QualByDepthV2" //snps.annotation :+= "QualByDepthV2"
snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile
snps.memoryLimit = Some(6)
//if (qscript.trigger != null) { //if (qscript.trigger != null) {
// snps.trigger_min_confidence_threshold_for_calling = Some(30) // snps.trigger_min_confidence_threshold_for_calling = Some(30)
// snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger) // snps.rodBind :+= RodBind("trigger", "VCF", qscript.trigger)
@ -320,44 +320,44 @@ class fullCallingPipeline extends QScript {
// 3.i generate gaussian clusters on the masked vcf // 3.i generate gaussian clusters on the masked vcf
// todo -- args for annotations? // todo -- args for annotations?
// todo -- args for resources (properties file) // todo -- args for resources (properties file)
val clusters = new GenerateVariantClusters with CommandLineGATKArgs // val clusters = new GenerateVariantClusters with CommandLineGATKArgs
clusters.jobOutputFile = new File(".queue/logs/SNPCalling/Clusters.out") // clusters.jobOutputFile = new File(".queue/logs/SNPCalling/Clusters.out")
clusters.rodBind :+= RodBind("input", "VCF", masker.out) // clusters.rodBind :+= RodBind("input", "VCF", masker.out)
clusters.DBSNP = qscript.pipeline.getProject.getDbsnpFile // clusters.rodBind :+= RodBind("dbsnp", "ROD", qscript.pipeline.getProject.getDbsnpFile)
val clusters_clusterFile = swapExt("SnpCalls/IntermediateFiles",snps.out,".vcf",".cluster") // val clusters_clusterFile = swapExt("SnpCalls/IntermediateFiles",snps.out,".vcf",".cluster")
clusters.clusterFile = clusters_clusterFile // clusters.clusterFile = clusters_clusterFile
clusters.memoryLimit = Some(4) // clusters.memoryLimit = Some(4)
clusters.jobQueue = qscript.big_mem_queue // clusters.jobQueue = qscript.big_mem_queue
clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun") // clusters.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
clusters.analysisName = base+"_Cluster" // clusters.analysisName = base+"_Cluster"
// 3.ii apply gaussian clusters to the masked vcf // 3.ii apply gaussian clusters to the masked vcf
val recalibrate = new VariantRecalibrator with CommandLineGATKArgs // val recalibrate = new VariantRecalibrator with CommandLineGATKArgs
recalibrate.jobOutputFile = new File(".queue/logs/SNPCalling/Recalibrator.out") // recalibrate.jobOutputFile = new File(".queue/logs/SNPCalling/Recalibrator.out")
recalibrate.clusterFile = clusters.clusterFile // recalibrate.clusterFile = clusters.clusterFile
recalibrate.DBSNP = qscript.pipeline.getProject.getDbsnpFile // recalibrate.DBSNP = qscript.pipeline.getProject.getDbsnpFile
recalibrate.rodBind :+= RodBind("input", "VCF", masker.out) // recalibrate.rodBind :+= RodBind("input", "VCF", masker.out)
recalibrate.out = swapExt("SnpCalls",masker.out,".vcf",".recalibrated.vcf") // recalibrate.out = swapExt("SnpCalls",masker.out,".vcf",".recalibrated.vcf")
recalibrate.target_titv = qscript.target_titv // recalibrate.target_titv = qscript.target_titv
recalibrate.tranches_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.tranches") // recalibrate.tranches_file = swapExt("SnpCalls/IntermediateFiles", masker.out,".vcf",".recalibrate.tranches")
recalibrate.analysisName = base+"_VariantRecalibrator" // recalibrate.analysisName = base+"_VariantRecalibrator"
// 3.iii apply variant cuts to the clusters // 3.iii apply variant cuts to the clusters
val cut = new ApplyVariantCuts with CommandLineGATKArgs // val cut = new ApplyVariantCuts with CommandLineGATKArgs
cut.jobOutputFile = new File(".queue/logs/SNPCalling/VariantCuts.out") // cut.jobOutputFile = new File(".queue/logs/SNPCalling/VariantCuts.out")
cut.rodBind :+= RodBind("input", "VCF", recalibrate.out) // cut.rodBind :+= RodBind("input", "VCF", recalibrate.out)
cut.out = swapExt("SnpCalls",recalibrate.out,".vcf",".tranched.vcf") // cut.out = swapExt("SnpCalls",recalibrate.out,".vcf",".tranched.vcf")
cut.tranches_file = recalibrate.tranches_file //cut.tranches_file = recalibrate.tranches_file
// todo -- fdr inputs, etc // todo -- fdr inputs, etc
cut.fdr_filter_level = Some(1) // cut.fdr_filter_level = Some(1)
cut.analysisName = base+"_ApplyVariantCuts" // cut.analysisName = base+"_ApplyVariantCuts"
// 4. Variant eval the cut and the hand-filtered vcf files // 4. Variant eval the cut and the hand-filtered vcf files
val eval = new VariantEval with CommandLineGATKArgs val eval = new VariantEval with CommandLineGATKArgs
eval.jobOutputFile = new File(".queue/logs/SNPCalling/VariantEval.out") eval.jobOutputFile = new File(".queue/logs/SNPCalling/VariantEval.out")
eval.rodBind :+= RodBind("evalOptimized", "VCF", cut.out) // eval.rodBind :+= RodBind("evalOptimized", "VCF", cut.out)
eval.rodBind :+= RodBind("evalHandFiltered", "VCF", handFilter.out) eval.rodBind :+= RodBind("eval", "VCF", handFilter.out)
eval.evalModule ++= List("SimpleMetricsBySample", "CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator") eval.evalModule ++= List("SimpleMetricsBySample", "CountFunctionalClasses", "CompOverlap", "CountVariants", "TiTvVariantEvaluator")
eval.reportLocation = new File("SnpCalls", base+".eval") eval.reportLocation = new File("SnpCalls", base+".eval")
eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R) eval.reportType = Option(org.broadinstitute.sting.utils.report.VE2ReportFactory.VE2TemplateType.R)
@ -397,6 +397,6 @@ class fullCallingPipeline extends QScript {
} }
// add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval,adpr) // add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval,adpr)
add(mergeIndels,annotated,masker,handFilter,clusters,recalibrate,cut,eval) add(mergeIndels,annotated,masker,handFilter,eval)
} }
} }