From 5815348ebcfc62f693b3c1f09cf1c3f5c970fa72 Mon Sep 17 00:00:00 2001 From: chartl Date: Wed, 4 Aug 2010 20:05:27 +0000 Subject: [PATCH] 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 --- scala/qscript/fullCallingPipeline.q | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 6ef14372e..cf09621bb 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -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 \ No newline at end of file +run