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14 Commits (dc62685a2f3aa5e40f42e4f8a9a67a6007c811f8)

Author SHA1 Message Date
carneiro c7a51f0de7 fixed 1kg pilot dindel calls vcf file and combined all vcfs into one master dindel file. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5335 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-28 19:04:58 +00:00
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
carneiro 2a48ec1307 now only accepts intervals files if the user specifically requests to report bams at interval only. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5291 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-23 16:49:58 +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
depristo d97ed3e080 Comments for Mauricio 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5275 348d0f76-0448-11de-a6fe-93d51630548a
 2011-02-18 16:58:34 +00:00
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