gatk-3.8

Author	SHA1	Message	Date
carneiro	8ea71fd294	minor dataset chages. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5289 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-22 20:18:10 +00:00
carneiro	c61dd2f09f	data processing pipeline now has on the fly bam indexing (powered by Matt) some new parameters, Indel Cleaning with constrain movement and fixMates is gone. setting up methods development pipeline for some cosmetic changes. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5277 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-18 23:13:54 +00:00
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