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Added Dbsnp to Indel Realigner; added known indels rod-binding to realigner. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4576 348d0f76-0448-11de-a6fe-93d51630548a
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corin 2010-10-26 22:22:28 +00:00
parent e02aac0743
commit 6d7ed5781c
1 changed files with 2 additions and 0 deletions
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2
scala/qscript/fullCallingPipeline.q
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@ -124,6 +124,8 @@ class fullCallingPipeline extends QScript {
realigner.intervals = Nil
realigner.intervalsString = Nil
realigner.scatterCount = num_cleaner_scatter_jobs min contigs.size
realigner.DBSNP = qscript.pipeline.getProject.getDbsnpFile
realigner.rodbind :+= RodBind("indels", "VCF", swapExt(qscript.pipeline.getProject.getReferenceFile, "fasta", "1kg_pilot_indels.vcf")
// if scatter count is > 1, do standard scatter gather, if not, explicitly set up fix mates
if (realigner.scatterCount > 1) {