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11 Commits (fd5d1f9cfc19b5abaadad9f83851807f9b29503d)

Author SHA1 Message Date
carneiro fd5d1f9cfc minor cosmetic changes. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5322 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-25 21:56:35 +00:00
carneiro 81414a21dd dpp: back to using 4gb memory assuming all is right with IndelRealigner now. 
mdcp: Some class structural changes due to the inclusion of indel calls. ApplyCut now chooses the tranche differently for each dataset.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5319 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-25 19:21:02 +00:00
carneiro 6db3210387 the data processing pipeline needs more memory... 
directory updates in the methods pipeline.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5305 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 17:22:58 +00:00
carneiro 897a333aba Methods Development Pipeline now has the option of calling indels with the -indels parameter. Also updated some databases and the new NA12878 HiSeq hg19 that Tim just funneled to us, is updated and called. 
Small fixes on the data processing pipeline


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5304 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 17:12:55 +00:00
rpoplin 255cc246a2 Change in Methods development pipeline: dbsnp130 can't be used for anything, changed it to dbsnp129. Optimization for HaplotypeScore and the to-be-committed ReadRosRankSumTest in AlignmentUtils 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5301 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-24 16:09:03 +00:00
carneiro ecfb51bcd8 Few organizational changes, queue output is now categorized and hidden. Also changed NA12878.Wex to dbsnp 129. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5290 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-22 22:49:38 +00:00
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