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This is now running. Expect results in a few weeks when the ~7k jobs have percolated through the week queue. Pray gsa1 doesn't go down. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5593 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2011-04-07 21:12:59 +00:00
parent 6a26957b65
commit cc58e19621
1 changed files with 10 additions and 9 deletions
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19
scala/qscript/oneoffs/chartl/Exome_VQSR_FullSearch.q
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@ -42,10 +42,10 @@ class Exome_VQSR_FullSearch extends QScript {
mrb :+= RodBind("dbsnp","VCF",DBSNP_129,VQSR_DBSNP_TAG)
mrb :+= RodBind("HapMap3","VCF",HM3_SITES,VQSR_TAG_FT.format(hmSt,VQSR_HAPMAP_PRIOR))
mrb :+= RodBind("Omni","VCF",OMNI_CHIP,VQSR_TAG_FT.format(omSt,VQSR_OMNI_PRIOR))
VQSR_RODBINDS += (ext,mrb)
VQSR_RODBINDS += new Tuple2(ext,mrb)
}
val BAM_FILES : List[File] = asScalaList((new XReadLines(new File("/humgen/gsa-hphome1/chartl/projects/oneoffs/VQSR_Exome/resources/broad.bam.list"))).readLines).map(u => new File(u))
val BAM_FILES : List[File] = asScalaIterator((new XReadLines(new File("/humgen/gsa-hphome1/chartl/projects/oneoffs/VQSR_Exome/resources/broad.bam.list")))).map(u => new File(u)).toList
val REF : File = new File("/seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta")
val INTS : File = new File("/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list")
val EXPAND_INTS = 40
@ -60,7 +60,7 @@ class Exome_VQSR_FullSearch extends QScript {
this.memoryLimit = Some(4)
}
val ei : ExpandIntervals = new ExpandIntervals(INTS,1,EXPAND_INTSs, new File("Resources", SCRIPT_BASE_NAME + ".flanks.interval_list"), REF, "INTERVALS", "INTERVALS")
val ei : ExpandIntervals = new ExpandIntervals(INTS,1,EXPAND_INTS, new File("Resources", SCRIPT_BASE_NAME + ".flanks.interval_list"), REF, "INTERVALS", "INTERVALS")
ei.jobOutputFile = new File(".queue/logs/Overall/ExpandIntervals.out")
if (EXPAND_INTS > 0) {
@ -138,21 +138,22 @@ class Exome_VQSR_FullSearch extends QScript {
val directory = getPath(annotations,recalTogether)
for ( call_thresh <- VQSR_CALL_THRESH ) {
var filterQual = new VariantFiltration with CommandLineGATKArgs with ExpandedIntervals
filterQual.rodBind :+= new RodBind("variant","VCF",extractSNPs.outputVCF)
filterQual.filterExpression :+= "QUAL < %.1f".format(VQSR_CALL_THRESH)
filterQual.rodBind :+= new RodBind("variant","VCF",extractSNPs.outputVCF.getAbsoluteFile)
filterQual.filterExpression :+= "QUAL < %.1f".format(call_thresh)
filterQual.filterName :+= "LowQual"
filterQual.commandDirectory = directory
filterQual.out = new File(directory.getAbsolutePath+"/"+SCRIPT_BASE_NAME+".filterQual%.1f.vcf".format(VQSR_CALL_THRESH))
filterQual.out = new File(directory.getAbsolutePath+"/"+SCRIPT_BASE_NAME+".filterQual%.1f.vcf".format(call_thresh))
add(filterQual)
for ( vqsr_rb <- VQSR_RODBINDS.iterator ) {
trait VQSR_Args extends ContrastiveRecalibrator {
this.allPoly = true
this.analysisName = "VQSR_%s_%s_%d".format( annotations.reduceLeft( _ + "." + _), if ( recalTogether ) "true" else "false", call_thresh)
this.analysisName = "VQSR_%s_%s_%.1f".format( annotations.reduceLeft( _ + "." + _), if ( recalTogether ) "true" else "false", call_thresh)
this.commandDirectory = directory
this.use_annotation ++= annotations
this.tranche ++= SENSITIVITY
this.tranche ++= SENSITIVITY.map(u => ".1f".format(u))
this.rodBind :+= RodBind("inputData","VCF",filterQual.out)
this.rodBind ++= vqsr_rb._2
this.memoryLimit = Some(8)
}
val nameFormat = SCRIPT_BASE_NAME+".%1f.%s.".format(call_thresh,vqsr_rb._1)+"%s."
if ( recalTogether ) {
@ -168,7 +169,7 @@ class Exome_VQSR_FullSearch extends QScript {
var flanks = new ContrastiveRecalibrator with VQSR_Args
flanks.intervals :+= ei.outList
flanks.jarFile = GATK_JAR
flanks.memoryLimit = Some(4)
flanks.memoryLimit = Some(8)
flanks.reference_sequence = REF
flanks.tranchesFile = new File(nameFormat.format("flanks")+"tranche")
flanks.recalFile = new File(nameFormat.format("flanks")+"recal")