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Ugh! varout --> out 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4157 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-08-29 02:34:41 +00:00
parent d7edce31a2
commit 2ffa98aea5
1 changed files with 1 additions and 1 deletions
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2
scala/qscript/fullCallingPipeline.q
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@ -181,7 +181,7 @@ class fullCallingPipeline extends QScript {
annotated.rodBind :+= RodBind("variant", "VCF", snps.out)
annotated.rodBind :+= RodBind("refseq", "AnnotatorInputTable", qscript.refseqTable)
annotated.rodBind :+= RodBind("dbsnp", "AnnotatorInputTable", qscript.dbsnpTable)
annotated.vcfOutput = swapExt(new File(snps.variants_out),".vcf",".annotated.vcf").getAbsolutePath
annotated.vcfOutput = swapExt(snps.out,".vcf",".annotated.vcf").getAbsolutePath
annotated.select :+= "dbsnp.name,dbsnp.refUCSC,dbsnp.strand,dbsnp.observed,dbsnp.avHet"
annotated.rodToIntervalTrackName = "variant"