47 lines
1.3 KiB
Scala
Executable File
47 lines
1.3 KiB
Scala
Executable File
/*
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* Created by IntelliJ IDEA.
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* User: carneiro
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* Date: 3/29/11
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* Time: 5:31 PM
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*/
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package oneoffs.carneiro;
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import org.broadinstitute.sting.queue.QScript
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import org.broadinstitute.sting.queue.extensions.gatk._
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class QuickCCTest extends QScript {
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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(shortName="L", required=false)
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var intervals: List[String] = Nil
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val queueLogDir: String = ".qlog/"
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def script = {
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val cc = new CountCovariates()
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cc.reference_sequence = reference
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cc.input_file :+= input
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cc.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
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cc.intervalsString = intervals
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cc.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
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cc.scatterCount = 4
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cc.recal_file = new File("recal.csv")
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add(cc);
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}
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} |