86 lines
3.2 KiB
Scala
Executable File
86 lines
3.2 KiB
Scala
Executable File
import org.broadinstitute.sting.queue.QScript
|
|
import org.broadinstitute.sting.queue.extensions.gatk._
|
|
import org.broadinstitute.sting.queue.extensions.samtools.SamtoolsIndexFunction
|
|
|
|
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 FULL_BAM_LIST = new File("/humgen/1kg/processing/allPopulations_chr20_june_release/allPopulations.june.bam.list")
|
|
val MERGED_DIR = new File("/humgen/gsa-hpprojects/dev/depristo/oneOffProjects/manySampleUGPerformance/")
|
|
|
|
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);
|
|
//this.commandDirectory = new File("results");
|
|
}
|
|
|
|
def script = {
|
|
for (nSamples <- List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500)) {
|
|
val sublist = new SliceList(nSamples)
|
|
val mergeSublist = new MergeBAMs(sublist.list)
|
|
|
|
add(sublist)
|
|
add(mergeSublist)
|
|
add(new Index(mergeSublist.o) )
|
|
|
|
// SNP calling
|
|
add(new Call(sublist.list, nSamples, "dynamic_merge"))
|
|
add(new Call(mergeSublist.o, nSamples, "pre_merge"))
|
|
|
|
// SNP calling -- no annotations
|
|
add(new Call(sublist.list, nSamples, "dynamic_merge_no_annotations") { this.G :+= "None"; })
|
|
add(new Call(mergeSublist.o, nSamples, "pre_merge_no_annotations") { this.G :+= "None"; })
|
|
|
|
// CountLoci
|
|
add(new MyCountLoci(sublist.list, nSamples, "dynamic_merge"))
|
|
add(new MyCountLoci(mergeSublist.o, nSamples, "pre_merge"))
|
|
|
|
}
|
|
}
|
|
|
|
class Index(bamIn: File) extends SamtoolsIndexFunction {
|
|
this.jobQueue = "gsa"
|
|
bamFile = bamIn
|
|
}
|
|
|
|
class MergeBAMs(bamList: File) extends PrintReads with UNIVERSAL_GATK_ARGS {
|
|
this.memoryLimit = Some(3)
|
|
this.input_file :+= bamList
|
|
this.o = new File(MERGED_DIR + "/" + bamList.getName + ".bam")
|
|
}
|
|
|
|
class Call(@Input(doc="foo") bamList: File, n: Int, name: String) extends UnifiedGenotyper with UNIVERSAL_GATK_ARGS {
|
|
@Output(doc="foo") var outVCF: File = new File("%s.%d.%s.vcf".format(bamList.getName, n, name))
|
|
this.memoryLimit = Some(4)
|
|
this.input_file :+= bamList
|
|
this.jobQueue = "gsa"
|
|
this.stand_call_conf = Option(10.0)
|
|
this.o = outVCF
|
|
}
|
|
|
|
class MyCountLoci(@Input(doc="foo") bamList: File, n: Int, name: String) extends CountLoci with UNIVERSAL_GATK_ARGS {
|
|
@Output(doc="foo") var outFile: File = new File("%s.%d.%s.txt".format(bamList.getName, n, name))
|
|
this.memoryLimit = Some(4)
|
|
this.input_file :+= bamList
|
|
this.jobQueue = "gsa"
|
|
this.o = outFile
|
|
}
|
|
|
|
class SliceList(n: Int) extends CommandLineFunction {
|
|
@Output(doc="foo") var list: File = new File("bams.%d.list".format(n))
|
|
this.jobQueue = "gsa"
|
|
def commandLine = "head -n %d %s > %s".format(n, FULL_BAM_LIST, list)
|
|
}
|
|
}
|
|
|