6 Commits (acad3ada064b2c93fa4f3034eceac9da589b9f56)

Author	SHA1	Message	Date
carneiro	acad3ada06	changed baq to calculate_as_necessary. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5270 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-17 23:50:46 +00:00
carneiro	7f9ca6b28a	full data processing pipeline, now deleting intermediate files and performing both phases (per lane and combined) of the processing. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5269 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-17 23:34:00 +00:00
carneiro	497e9ab83b	too hasty... cleaning up debug messages ;) ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5257 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-17 02:11:03 +00:00
carneiro	b4da843c49	now processes either a single bam file or a list of bam files in parallel. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5256 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-17 02:07:22 +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	6d3b878dde	data processing pipeline script already does: ... . Local Indel Realignment . Mark Duplicates will do: . Base Quality Score Recalibration (soon) it's working with a single BAM for testing, but will work with a list of bam files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5250 348d0f76-0448-11de-a6fe-93d51630548a	2011-02-15 21:49:05 +00:00