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Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3941 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-08-04 20:05:27 +00:00
parent 86211b74e8
commit 5815348ebc
1 changed files with 10 additions and 3 deletions
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13
scala/qscript/fullCallingPipeline.q
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@ -45,7 +45,7 @@ class RealignerTargetCreator extends GatkFunctionLocal {
// step two: we need to clean each bam file - gather will fix mates
/////////////////////////////////////////////////
class IndelRealigner extends GatkFunctionLocal {
class IndelRealigner extends GatkFunction {
@Input(doc="Intervals to clean")
var intervalsToClean: File = _
@Scatter(classOf[ContigScatterFunction])
@ -57,6 +57,12 @@ class IndelRealigner extends GatkFunctionLocal {
this.javaTmpDir = parseArgs("-tmpdir") // todo -- hack, move into script or something
override def freeze = {
this.intervals = contigIntervals
this.jobQueue = "long"
super.freeze
}
def commandLine = gatkCommandLine("IndelRealigner") + "--output %s -targetIntervals %s -L %s".format(cleanedBam,intervalsToClean,contigIntervals)
}
@ -267,7 +273,8 @@ def endToEnd(base: String, snps: UnifiedGenotyper, indels: UnifiedGenotyperIndel
snps.callConf = 30
snps.trigger = new File(parseArgs("-trigger"))
// todo -- hack -- get this from the command line, or properties
snps.compTracks :+= ( "comp1KG_CEU",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/100328.CEU.hg18.sites.vcf") )
snps.compTracks :+= ( "comp1KG_CEU",new File("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/1kg_pilot1_projectCalls/CEU.low_coverage.2010_07.sites.hg18.vcf.gz") )
snps.compTracks :+= ( "comp1KG_ALL",new File(parseArgs("-trigger") ) )
snps.scatterCount = 100
indels.indelVCF = new File(base+".indels.vcf")
indels.scatterCount = 100
@ -317,4 +324,4 @@ endToEnd(uncleanedBase,uncleanSNPCalls,uncleanIndelCalls)
endToEnd(cleanedBase,cleanSNPCalls,cleanIndelCalls)
setParams
run
run