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Script to identify mendelian violations in the CEU Trio and follow up with supposedly incorrect SNP calls 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5744 348d0f76-0448-11de-a6fe-93d51630548a
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carneiro 2011-05-03 21:19:42 +00:00
parent e2b9227d8d
commit 8bb92160b5
1 changed files with 56 additions and 0 deletions
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scala/qscript/oneoffs/carneiro/mendelianViolation.scala 100755
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import java.io.File
import org.broadinstitute.sting.commandline.Argument
import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind}
import org.broadinstitute.sting.queue.QScript
/*
* Created by IntelliJ IDEA.
* User: carneiro
* Date: 4/12/11
* Time: 11:24 AM
*/
class mendelianViolation extends QScript
{
@Argument(shortName="trio", doc="input trio VCF file", required=false)
var trio: File = new File("/home/radon00/carneiro/prj/trio/analysis/calls/CEUTrio.WEx.recalibrated.vcf")
@Argument(shortName="daughter", doc="daughter input VCF file", required=false)
var daughter: File = "/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/NA12878/chart/sting/NA12878.HiSeq19.recalibrated.hapmapCut.vcf"
@Argument(shortName="family", doc="family string", required=false)
var family: String = "NA12891+NA12892=NA12878"
@Argument(shortName="mvq", doc="mendelian violation quality", required=false)
var mvq: Double = 20
@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=false)
var GATKjar: File = new File("/humgen/gsa-scr1/carneiro/stable/dist/GenomeAnalysisTK.jar")
def script = {
val reference = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
val trioViolations = "trio_violations.vcf"
val daughterViolations = "daughter_violations.vcf"
val mv = new SelectVariants()
mv.rodBind :+= RodBind("variant", "VCF", trio)
mv.family = family
mv.reference_sequence = reference
mv.mvq = mvq
mv.out = trioViolations
mv.jarFile = GATKjar
mv.memoryLimit = 4
val intersection = new SelectVariants()
intersection.rodBind :+= RodBind("variant", "VCF", daughter)
intersection.rodBind :+= RodBind("conc","VCF", trioViolations)
intersection.reference_sequence = reference
intersection.conc = "conc"
intersection.out = daughterViolations
intersection.jarFile = GATKjar
intersection.memoryLimit = 4
add(mv, intersection)
}
}