From 9132c98eecda383fe4756af9f30e401fdacf6d18 Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 29 Jul 2010 22:04:02 +0000 Subject: [PATCH] Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3904 348d0f76-0448-11de-a6fe-93d51630548a --- scala/qscript/fullCallingPipeline.q | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 2cd3aed45..6ef14372e 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -26,7 +26,11 @@ def parseArgs(flag: String): String = { ///////////////////////////////////////////////// // todo -- make me less of a hack that makes Khalid cry abstract class GatkFunctionLocal extends GatkFunction { - this.intervals = QScript.inputs("interval_list").head + if ( QScript.inputs("interval_list").size > 0 ) { + this.intervals = QScript.inputs("interval_list").head + } else { + this.intervals = QScript.inputs("interval.list").head + } } class RealignerTargetCreator extends GatkFunctionLocal { @@ -189,7 +193,7 @@ class GenomicAnnotator extends GatkFunctionLocal { @Output(doc="A genomically annotated VCF file") var annotatedVCF: File = _ - def commandLine = gatkCommandLine("GenomicAnnotator") + " -B variant,VCF,%s -B refseq,AnnotatorInputTable,%s -B dbsnp,AnnotatorInputTable,%s -vcf %s -s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet".format(inputVCF,refseqTable,dbsnpTable,annotatedVCF) + def commandLine = gatkCommandLine("GenomicAnnotator") + " -B variant,VCF,%s -B refseq,AnnotatorInputTable,%s -B dbsnp,AnnotatorInputTable,%s -vcf %s -s dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet -BTI variant".format(inputVCF,refseqTable,dbsnpTable,annotatedVCF) } ///////////////////////////////////////////////// @@ -264,16 +268,16 @@ def endToEnd(base: String, snps: UnifiedGenotyper, indels: UnifiedGenotyperIndel 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.scatterCount = 20 + snps.scatterCount = 100 indels.indelVCF = new File(base+".indels.vcf") - indels.scatterCount = 20 + indels.scatterCount = 100 // 1b. genomically annotate SNPs -- slow, but scatter it val annotated = new GenomicAnnotator annotated.inputVCF = snps.rawVCF annotated.refseqTable = new File(parseArgs("-refseqTable")) annotated.dbsnpTable = new File(parseArgs("-dbsnpTable")) annotated.annotatedVCF = swapExt(snps.rawVCF,".vcf",".annotated.vcf") - annotated.scatterCount = 20 + annotated.scatterCount = 100 // 2.a filter on cluster and near indels val masker = new VariantFiltration masker.unfilteredVCF = annotated.annotatedVCF