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Evaluates within standard target and expanded target separately. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5268 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran 2011-02-17 23:04:24 +00:00
parent 92c82200c9
commit 4f83151c4e
1 changed files with 30 additions and 15 deletions
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45
scala/qscript/playground/FullCallingPipeline.q
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@ -264,20 +264,31 @@ class FullCallingPipeline extends QScript {
annotated.rodBind :+= RodBind("variant", "VCF", combineAll.out) annotated.rodBind :+= RodBind("variant", "VCF", combineAll.out)
annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.pipeline.getProject.getRefseqTable) annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.pipeline.getProject.getRefseqTable)
annotated.out = new File(base + ".snps_and_indels.filtered.annotated.vcf") annotated.out = new File(base + ".snps_and_indels.filtered.annotated.vcf")
//annotated.out = swapExt("VariantCalls", combineAll.out, ".vcf", ".annotated.vcf")
// Variant eval the cut and the hand-filtered vcf files // Variant eval the standard region
val smallEval = new VariantEval with CommandLineGATKArgs with ExpandedIntervals val stdEval = new VariantEval with CommandLineGATKArgs
smallEval.analysisName = base+"_VariantEval" stdEval.analysisName = base+"_VariantEval"
smallEval.jobOutputFile = new File(".queue/logs/Overall/VariantEval.out") stdEval.jobOutputFile = new File(".queue/logs/Overall/VariantEval.std.out")
smallEval.noST = true stdEval.noST = true
smallEval.noEV = true stdEval.noEV = true
smallEval.evalModule ++= List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants") stdEval.evalModule ++= List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
smallEval.stratificationModule ++= List("EvalRod", "Novelty") stdEval.stratificationModule ++= List("EvalRod", "CompRod", "Novelty")
smallEval.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getEvalDbsnpType, qscript.pipeline.getProject.getEvalDbsnp) stdEval.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getEvalDbsnpType, qscript.pipeline.getProject.getEvalDbsnp)
smallEval.rodBind :+= RodBind("eval", "VCF", annotated.out) stdEval.rodBind :+= RodBind("eval", "VCF", annotated.out)
smallEval.out = swapExt(annotated.out, ".vcf", ".eval") stdEval.out = swapExt(annotated.out, ".vcf", ".eval")
//smallEval.out = new File("VariantCalls", base+".gatkreport")
// Variant eval the flanking region
val flanksEval = new VariantEval with CommandLineGATKArgs
flanksEval.analysisName = base+"_VariantEval"
flanksEval.jobOutputFile = new File(".queue/logs/Overall/VariantEval.flanks.out")
flanksEval.intervals = List(ei.outList)
flanksEval.noST = true
flanksEval.noEV = true
flanksEval.evalModule ++= List("SimpleMetricsByAC", "TiTvVariantEvaluator", "CountVariants")
flanksEval.stratificationModule ++= List("EvalRod", "CompRod", "Novelty")
flanksEval.rodBind :+= RodBind("dbsnp", qscript.pipeline.getProject.getEvalDbsnpType, qscript.pipeline.getProject.getEvalDbsnp)
flanksEval.rodBind :+= RodBind("eval", "VCF", annotated.out)
flanksEval.out = swapExt(annotated.out, ".vcf", ".flanks.eval")
// Make the bam list // Make the bam list
val listOfBams = new File("Resources", base +".BamFiles.list") val listOfBams = new File("Resources", base +".BamFiles.list")
@ -288,7 +299,11 @@ class FullCallingPipeline extends QScript {
writeBamList.inputFiles = bamFiles writeBamList.inputFiles = bamFiles
writeBamList.listFile = listOfBams writeBamList.listFile = listOfBams
add(indels, filteredIndels, snps, filteredSNPs, combineAll, annotated, smallEval, writeBamList) add(indels, filteredIndels, snps, filteredSNPs, combineAll, annotated, stdEval, writeBamList)
if (qscript.expandIntervals > 0) {
add(flanksEval)
}
// Run the ADPR and make pretty stuff // Run the ADPR and make pretty stuff
if (qscript.tearScript != null) { if (qscript.tearScript != null) {
@ -311,7 +326,7 @@ class FullCallingPipeline extends QScript {
adpr.bamlist = listOfBams adpr.bamlist = listOfBams
adpr.yaml = qscript.yamlFile.getAbsoluteFile adpr.yaml = qscript.yamlFile.getAbsoluteFile
adpr.script = qscript.tearScript adpr.script = qscript.tearScript
adpr.evalroot = smallEval.out adpr.evalroot = stdEval.out
adpr.jobOutputFile = new File(".queue/logs/Overall/ADPR.out") adpr.jobOutputFile = new File(".queue/logs/Overall/ADPR.out")
adpr.tearsheet = new File("VariantCalls", base + ".tearsheet.pdf") adpr.tearsheet = new File("VariantCalls", base + ".tearsheet.pdf")