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Author SHA1 Message Date
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