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Removing old arguments. We'll now be running with the defaults. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4811 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-12-09 18:58:56 +00:00
parent fabb42924c
commit 27acede64d
1 changed files with 3 additions and 3 deletions
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6
scala/qscript/fullCallingPipeline.q
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@ -209,9 +209,9 @@ class fullCallingPipeline extends QScript {
snps.input_file = bamFiles snps.input_file = bamFiles
snps.group :+= "Standard" snps.group :+= "Standard"
snps.out = new File("SnpCalls", base+".vcf") snps.out = new File("SnpCalls", base+".vcf")
snps.standard_min_confidence_threshold_for_emitting = Some(10) //snps.standard_min_confidence_threshold_for_emitting = Some(10)
snps.min_mapping_quality_score = Some(20) //snps.min_mapping_quality_score = Some(20)
snps.min_base_quality_score = Some(20) //snps.min_base_quality_score = Some(20)
snps.downsample_to_coverage = Some(qscript.downsampling_coverage) snps.downsample_to_coverage = Some(qscript.downsampling_coverage)
//snps.annotation :+= "QualByDepthV2" //snps.annotation :+= "QualByDepthV2"
snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile snps.DBSNP = qscript.pipeline.getProject.getDbsnpFile