50 lines
1.4 KiB
Scala
Executable File
50 lines
1.4 KiB
Scala
Executable File
/*
|
|
* Created by IntelliJ IDEA.
|
|
* User: carneiro
|
|
* Date: 3/29/11
|
|
* Time: 5:31 PM
|
|
*/
|
|
package oneoffs.carneiro;
|
|
|
|
import org.broadinstitute.sting.queue.QScript
|
|
import org.broadinstitute.sting.queue.extensions.gatk._
|
|
|
|
class QuickCCTest extends QScript {
|
|
qscript =>
|
|
|
|
@Input(doc="path to GenomeAnalysisTK.jar", shortName="gatk", required=true)
|
|
var GATKjar: File = _
|
|
|
|
@Input(doc="input BAM file - or list of BAM files", shortName="i", required=true)
|
|
var input: File = _
|
|
|
|
@Input(doc="Reference fasta file", shortName="R", required=false)
|
|
var reference: File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
|
|
|
|
@Input(doc="dbsnp ROD to use (VCF)", shortName="D", required=false)
|
|
var dbSNP: File = new File("/humgen/gsa-hpprojects/GATK/data/dbsnp_132_b37.leftAligned.vcf")
|
|
|
|
@Input(shortName="L", required=false)
|
|
var intervals: List[String] = Nil
|
|
|
|
|
|
val queueLogDir: String = ".qlog/"
|
|
|
|
|
|
def script = {
|
|
|
|
val recal = new File("recal.csv")
|
|
|
|
val cc = new CountCovariates()
|
|
cc.reference_sequence = reference
|
|
cc.input_file :+= input
|
|
cc.rodBind :+= RodBind("dbsnp", "VCF", dbSNP)
|
|
cc.intervalsString = intervals
|
|
cc.covariate ++= List("ReadGroupCovariate", "QualityScoreCovariate", "CycleCovariate", "DinucCovariate")
|
|
cc.scatterCount = 4
|
|
cc.recal_file = recal
|
|
cc.memoryLimit = 4
|
|
|
|
add(cc);
|
|
}
|
|
} |