carneiro 35a4f1e366 .Added VariantEval as an optional step in the pipeline. ... .Lifted to HapMap 3.3 .Lifted to dbSNP 132 where possible. .Added the CEU-Trio WEx(hg19) dataset .Added some options to the pipeline You can now use : -dataset WEX -dataset HiSeq ... to choose which datasets to run through the pipeline. You can now without BAQ and indel mask: -noBAQ -noMASK Choose not to run the gold standard comparison analysis: -skipGoldStandard Activate the VariantEval walker analysis on the Recalibrated vcf: -eval The default behavior is to run exactly like it used to, so this version shouldn't change the way you used to use the pipeline. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5004 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-14 21:55:02 +00:00
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ASHGcalling.scala	By popular demand I'm adding the qscript I used to do the 660 bamfile 1000G calling for ASHG. It does cleaning, BAQing, and merging in 3mb chunks genome-wide then calls SNPs on those temporary bams.	2010-12-17 18:49:03 +00:00
MethodsDevelopmentCallingPipeline.scala	.Added VariantEval as an optional step in the pipeline.	2011-01-14 21:55:02 +00:00
variantRecalibrator.scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00