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10 Commits (9ddee96f935b6cdbeab3511d1494feb70b2c22dc)

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
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 5f10fffa47 merge intervals now prints a sorted list in the end. 
added the ccs datasets to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5233 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 20:57:59 +00:00
carneiro 50c2fa3c3a this -1 made ALL the difference in the world. Minor bug fix. 
Regular updates to the pbCalling pipeline.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5232 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-11 19:25:09 +00:00
carneiro 9c2c5efe35 a modified version of the Methods Development calling pipeline made to work with pacbio data. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5225 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-10 16:06:50 +00:00