45 lines
1.7 KiB
Scala
45 lines
1.7 KiB
Scala
import java.io.File
|
|
import org.broadinstitute.sting.commandline.Argument
|
|
import org.broadinstitute.sting.queue.QScript
|
|
import org.broadinstitute.sting.queue.extensions.gatk._
|
|
import org.broadinstitute.sting.queue.extensions.samtools._
|
|
|
|
class ManySampleUGPerformanceTesting extends QScript {
|
|
@Argument(doc="gatkJarFile", required=false)
|
|
var gatkJarFile: File = new File("/home/radon01/depristo/dev/GenomeAnalysisTKStable/trunk/dist/GenomeAnalysisTK.jar")
|
|
|
|
@Argument(shortName = "R", doc="ref", required=false)
|
|
var referenceFile: File = new File("/humgen/1kg/reference/human_g1k_v37.fasta")
|
|
|
|
val TARGET_INTERVAL = "my.intervals"
|
|
val TEST_BAM_LIST = new File("ten.bam.list")
|
|
val FULL_BAM_LIST = new File("/humgen/1kg/processing/allPopulations_chr20_june_release/allPopulations.june.bam.list")
|
|
val BAM_LIST = FULL_BAM_LIST
|
|
val HM3 = new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Validated/HapMap/3.2/genotypes_r27_nr.hg19_fwd.vcf")
|
|
|
|
trait UNIVERSAL_GATK_ARGS extends CommandLineGATK {
|
|
this.logging_level = "INFO";
|
|
this.jarFile = gatkJarFile;
|
|
this.intervals = List(new File(TARGET_INTERVAL));
|
|
this.reference_sequence = referenceFile;
|
|
this.jobQueue = "gsa";
|
|
this.et = Option(org.broadinstitute.sting.gatk.phonehome.GATKRunReport.PhoneHomeOption.STANDARD);
|
|
this.dcov = Option(50);
|
|
}
|
|
|
|
def script = {
|
|
// SNP calling
|
|
add(new MyQSample(BAM_LIST));
|
|
}
|
|
|
|
class MyQSample(@Input(doc="foo") bamList: File) extends QSample with UNIVERSAL_GATK_ARGS {
|
|
this.memoryLimit = Some(4)
|
|
this.input_file :+= bamList
|
|
//this.BTI = "genotypes"
|
|
this.nt = Option(10)
|
|
this.rodBind :+= RodBind("genotypes", "VCF", HM3)
|
|
this.o = new File("%s.qsample".format(bamList.getName))
|
|
}
|
|
}
|
|
|