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Minor modifications to fCP 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4294 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-09-16 18:29:24 +00:00
parent de56568ce4
commit c581bd2d84
1 changed files with 5 additions and 2 deletions
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7
scala/qscript/fullCallingPipeline.q
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@ -127,7 +127,10 @@ class fullCallingPipeline extends QScript {
// step through the un-indel-cleaned graph: // step through the un-indel-cleaned graph:
// 1a. call snps and indels // 1a. call snps and indels
val snps = new UnifiedGenotyper with CommandLineGATKArgs val snps = new UnifiedGenotyper with CommandLineGATKArgs
snps.input_file = bamFiles for ( bam <- bamFiles ) {
snps.input_file :+= bam.toNamedFile
}
//snps.input_file = bamFiles
snps.group :+= "Standard" snps.group :+= "Standard"
snps.out = new File(base+".vcf") snps.out = new File(base+".vcf")
snps.standard_min_confidence_threshold_for_emitting = Some(10) snps.standard_min_confidence_threshold_for_emitting = Some(10)
@ -157,7 +160,7 @@ class fullCallingPipeline extends QScript {
var loopNo = 0 var loopNo = 0
var priority = "" var priority = ""
for ( bam <- bamFiles ) { for ( bam <- bamFiles ) {
val indel = new IndelGenotyperV2 with CommandLineGATKArgs var indel = new IndelGenotyperV2 with CommandLineGATKArgs
indel.input_file :+= bam indel.input_file :+= bam
indel.out = swapExt(bam,".bam",".indels.vcf") indel.out = swapExt(bam,".bam",".indels.vcf")
indel.downsample_to_coverage = Some(500) indel.downsample_to_coverage = Some(500)