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Author SHA1 Message Date
carneiro 50c870cfce Data Processing Pipeline: local indel realignment, mark duplicates and BQSR. Done. 
Pacbio pipeline: now all pacbio bams have baq annotated in so running UG is uber fast.

Methods pipeline: minor cosmetic changes.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5253 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-16 17:22:30 +00:00
carneiro 87e19a17ae small updates to the variant eval part of the pipeline, some updates to the pacbio specific pipeline. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5244 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-15 16:19:07 +00:00
carneiro c630701a76 Following Ryan's suggestion, I am moving the Methods Development Calling pipeline to the Core. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5226 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-10 17:36:05 +00:00