70 lines
2.5 KiB
Scala
Executable File
70 lines
2.5 KiB
Scala
Executable File
import org.broadinstitute.sting.queue.extensions.gatk.{RealignerTargetCreator, RodBind, IndelRealigner}
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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: 3/17/11
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* Time: 11:29 AM
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* To change this template use File | Settings | File Templates.
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*/
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class justClean extends QScript {
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@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
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var GATKjar: File = _
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@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
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var input: File = _
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@Input(doc="Reference fasta file", shortName="R", required=false)
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var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
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@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
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var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
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@Input(doc="extra VCF files to use as reference indels for Indel Realignment", shortName="indels", required=false)
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var indels: File = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/AFR+EUR+ASN+1KG.dindel_august_release_merged_pilot1.20110126.sites.vcf")
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val queueLogDir: String = ".qlog/"
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def script = {
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val outBam = swapExt(input, ".bam", ".Qclean.bam")
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val tIntervals = swapExt(input, ".bam", ".Qall_indels.intervals")
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val target = new RealignerTargetCreator()
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target.input_file :+= input
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target.out = tIntervals
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target.reference_sequence = reference
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target.mismatchFraction = Some(0.0)
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target.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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target.rodBind :+= RodBind("indels", "VCF", indels)
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target.memoryLimit = Some(6)
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target.jobName = queueLogDir + tIntervals + ".atarget"
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target.jarFile = GATKjar
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target.scatterCount = 84
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val clean = new IndelRealigner()
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clean.input_file :+= input
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clean.targetIntervals = tIntervals
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clean.out = outBam
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clean.reference_sequence = reference
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clean.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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clean.rodBind :+= RodBind("indels", "VCF", indels)
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clean.doNotUseSW = true
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clean.compress = Some(0)
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clean.U = Some(org.broadinstitute.sting.gatk.arguments.ValidationExclusion.TYPE.NO_READ_ORDER_VERIFICATION) // todo -- update clean with the last consensus between Tim, Matt and Eric. This is ugly!
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clean.jobName = queueLogDir + outBam + ".clean"
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clean.jarFile = GATKjar
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clean.memoryLimit = Some(6)
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clean.scatterCount = 84
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add(target, clean);
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}
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}
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