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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
This commit is contained in:
chartl 2010-07-29 22:04:02 +00:00
parent 54d93f63d2
commit 9132c98eec
1 changed files with 9 additions and 5 deletions
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14
scala/qscript/fullCallingPipeline.q
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@ -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