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Updates Omni path and removes a typo 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5673 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
corin 2011-04-21 04:17:13 +00:00
parent 0007481890
commit 9f006be425
1 changed files with 7 additions and 6 deletions
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13
scala/qscript/playground/wgs.q
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@ -42,7 +42,7 @@ class WGSpipeline extends QScript {
val hapmap = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.3/sites_r27_nr.b37_fwd.vcf"
val g1k = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/ALL.low_coverage.2010_07.hg19.vcf"
val omni = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/764samples.deduped.b37.annot.vcf"
val omni = "/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/Omni2.5_chip/Omni25_sites_1525_samples.b37.vcf"
private var pipeline: Pipeline = _
@ -141,7 +141,7 @@ class WGSpipeline extends QScript {
combineVCFs.jobOutputFile = new File ("/humgen/gsa-pipeline/" +projectBase + ".combine.out")
combineVCFs.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.PRIORITIZE
combineVCFs.intervalsString :+= "20:1-63025520" ///TODO impliment only using the chr 20 or nothing if freeze
combineVCFs.assumeIdenticalSamples = true
val sv = new SelectVariants with CommandLineGATKArgs
@ -164,17 +164,17 @@ class WGSpipeline extends QScript {
val recombine = new CombineVariants with CommandLineGATKArgs
recombine.rodBind :+= RodBind("indels", "VCF", sv.out)
recombine.rodBind :+= RodBind("all", "VCF", combineVCFs.out)
recombine.priority = "indels, all"
recombine.priority = "indels,all"
recombine.genotypemergeoption = org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils.GenotypeMergeType.PRIORITIZE
recombine.out = swapExt(combineVCFs.out, "vcf", "filtered.vcf")
recombine.jobName = qscript.project + ".recombine"
recombine.jobOutputFile = swapExt(combineVCFs.jobOutputFile, "combine.out", "recombine.out")
val cr = new ContrastiveRecalibrator with CommandLineGATKArgs
cr.rodBind :+= RodBind("hapmap", "VCF", qscript.hapmap)
cr.rodBind :+= RodBind("1kg", "VCF", qscript.omni)
cr.rodBind :+= RodBind("hapmap","VCF", qscript.hapmap, "training=true, prior=3.0")
cr.rodBind :+= RodBind("1kg", "VCF", qscript.omni, "training=true, prior=3.0")
cr.rodBind :+= RodBind("input", "VCF", recombine.out)
cr.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
cr.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP, "known=true")
cr.use_annotation ++= List("QD", "SB", "HaplotypeScore", "HRun")
cr.jobName = qscript.project + ".cr"
cr.jobOutputFile = swapExt(combineVCFs.jobOutputFile, ".combine.out", ".cr.out")
@ -202,6 +202,7 @@ class WGSpipeline extends QScript {
stdEval.rodBind :+= RodBind("dbsnp", "VCF", qscript.dbSNP)
stdEval.rodBind :+= RodBind("eval", "VCF", ar.out)
stdEval.out = swapExt(ar.out, ".vcf", ".eval")
stdEval.tranchesFile = cr.tranches_file
add(combineVCFs, filter, sv, recombine, cr, ar, stdEval)
}