57 lines
1.9 KiB
Scala
Executable File
57 lines
1.9 KiB
Scala
Executable File
import java.io.File
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import org.broadinstitute.sting.commandline.Argument
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import org.broadinstitute.sting.queue.extensions.gatk.{SelectVariants, RodBind}
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import org.broadinstitute.sting.queue.QScript
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/*
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* Created by IntelliJ IDEA.
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* User: carneiro
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* Date: 4/12/11
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* Time: 11:24 AM
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*/
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class mendelianViolation extends QScript
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{
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@Argument(shortName="trio", doc="input trio VCF file", required=false)
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var trio: File = new File("/home/radon00/carneiro/prj/trio/analysis/calls/CEUTrio.WEx.recalibrated.vcf")
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@Argument(shortName="daughter", doc="daughter input VCF file", required=false)
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var daughter: File = "/humgen/gsa-hpprojects/dev/rpoplin/perfectCalls/NA12878/chart/sting/NA12878.HiSeq19.recalibrated.hapmapCut.vcf"
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@Argument(shortName="family", doc="family string", required=false)
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var family: String = "NA12891+NA12892=NA12878"
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@Argument(shortName="mvq", doc="mendelian violation quality", required=false)
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var mvq: Double = 20
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@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=false)
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var GATKjar: File = new File("/humgen/gsa-scr1/carneiro/stable/dist/GenomeAnalysisTK.jar")
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def script = {
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val reference = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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val trioViolations = "trio_violations.vcf"
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val daughterViolations = "daughter_violations.vcf"
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val mv = new SelectVariants()
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mv.rodBind :+= RodBind("variant", "VCF", trio)
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mv.family = family
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mv.reference_sequence = reference
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mv.mvq = mvq
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mv.out = trioViolations
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mv.jarFile = GATKjar
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mv.memoryLimit = 4
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val intersection = new SelectVariants()
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intersection.rodBind :+= RodBind("variant", "VCF", daughter)
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intersection.rodBind :+= RodBind("conc","VCF", trioViolations)
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intersection.reference_sequence = reference
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intersection.conc = "conc"
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intersection.out = daughterViolations
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intersection.jarFile = GATKjar
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intersection.memoryLimit = 4
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add(mv, intersection)
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}
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}
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