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Computes how well a genotype chip covers a reference panel 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5806 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2011-05-14 15:07:28 +00:00
parent 5e9c0d00c6
commit 9423652ad8
1 changed files with 11 additions and 7 deletions
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18
scala/qscript/oneoffs/depristo/AssessChipCoverageOfPanel.q
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@ -47,14 +47,12 @@ class AssessChipCoverageOfPanel extends QScript {
this.G = List("none") this.G = List("none")
this.A :+= "ChromosomeCounts" this.A :+= "ChromosomeCounts"
this.nsl = true this.nsl = true
this.nt = 4
// make sure we have the right intervals // make sure we have the right intervals
this.BTIMR = org.broadinstitute.sting.utils.interval.IntervalSetRule.INTERSECTION this.BTIMR = org.broadinstitute.sting.utils.interval.IntervalSetRule.INTERSECTION
} }
// todo -- include AF from 1000G in annotation
// todo -- distance from SNP to nearest chip SNP
class EvalCalls(@Input vcf: File) extends VariantEval with GATKArgs { class EvalCalls(@Input vcf: File) extends VariantEval with GATKArgs {
this.o = swapExt(vcf, ".vcf", ".vcf.eval") this.o = swapExt(vcf, ".vcf", ".vcf.eval")
this.rodBind :+= RodBind("eval", "VCF", vcf) this.rodBind :+= RodBind("eval", "VCF", vcf)
@ -67,23 +65,29 @@ class AssessChipCoverageOfPanel extends QScript {
this.rodBind :+= RodBind("variant", "VCF", vcf) this.rodBind :+= RodBind("variant", "VCF", vcf)
this.rodBind :+= RodBind("compOMNI", "VCF", OMNI_VCF) this.rodBind :+= RodBind("compOMNI", "VCF", OMNI_VCF)
this.rodBind :+= RodBind("compHapMap3", "VCF", HM3_VCF) this.rodBind :+= RodBind("compHapMap3", "VCF", HM3_VCF)
this.rodBind :+= RodBind("panel", "VCF", panelVCF)
this.expression = List("panel.AC", "panel.AN", "panel.AF")
} }
class MakeTable(@Input vcf: File, @Output table: File) extends VariantsToTable with GATKArgs { class MakeTable(@Input vcf: File) extends VariantsToTable with GATKArgs {
@Output val table = new File(swapExt(vcf, ".vcf", ".vcf.table"))
this.o = table this.o = table
this.rodBind :+= RodBind("variants", "VCF", vcf) this.rodBind :+= RodBind("variants", "VCF", vcf)
this.allowMissingData = true this.allowMissingData = true
this.fields = List("CHROM", "POS", "REF", "ALT", "TRANSITION", "HapMap3", "OMNI", "AC", "AN", "AF") this.fields = List("CHROM", "POS", "REF", "ALT", "TRANSITION", "HapMap3",
"OMNI", "AC", "AN", "AF", "panel.AC", "panel.AN", "panel.AF")
} }
def script = { def script = {
val genotyped = new File(swapExt(bam, ".bam", "_genotyped_at." + panelVCF.getName).getName) val genotyped = new File(swapExt(bam, ".bam", "_genotyped_at." + panelVCF.getName).getName)
val panelAnnotated = new File(swapExt(panelVCF, ".vcf", ".annotated.vcf"))
val annotated = new File(swapExt(genotyped, ".vcf", ".annotated.vcf")) val annotated = new File(swapExt(genotyped, ".vcf", ".annotated.vcf"))
val table = new File(swapExt(annotated, ".vcf", ".vcf.table"))
add(new GenotypeBAMAtSites(bam, panelVCF, genotyped)) add(new GenotypeBAMAtSites(bam, panelVCF, genotyped))
add(new AnnotateCalls(panelVCF, panelAnnotated))
add(new AnnotateCalls(genotyped, annotated)) add(new AnnotateCalls(genotyped, annotated))
add(new EvalCalls(annotated)) add(new EvalCalls(annotated))
add(new MakeTable(annotated, table)) add(new MakeTable(annotated))
add(new MakeTable(panelAnnotated))
} }
} }