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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
This commit is contained in:
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.A :+= "ChromosomeCounts"
this.nsl = true
this.nt = 4
// make sure we have the right intervals
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 {
this.o = swapExt(vcf, ".vcf", ".vcf.eval")
this.rodBind :+= RodBind("eval", "VCF", vcf)
@ -67,23 +65,29 @@ class AssessChipCoverageOfPanel extends QScript {
this.rodBind :+= RodBind("variant", "VCF", vcf)
this.rodBind :+= RodBind("compOMNI", "VCF", OMNI_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.rodBind :+= RodBind("variants", "VCF", vcf)
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 = {
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 table = new File(swapExt(annotated, ".vcf", ".vcf.table"))
add(new GenotypeBAMAtSites(bam, panelVCF, genotyped))
add(new AnnotateCalls(panelVCF, panelAnnotated))
add(new AnnotateCalls(genotyped, annotated))
add(new EvalCalls(annotated))
add(new MakeTable(annotated, table))
add(new MakeTable(annotated))
add(new MakeTable(panelAnnotated))
}
}