96628457cb
pacbio calling pipeline also using VQSR2 now, minor updates on the other pipelines to get the papuans through.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5479 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 22:06:52 +00:00
c9442e4b21
now merging bam files per sample and processing according to cleaning options.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5477 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 21:31:29 +00:00
18fac5112c
first step towards the new sample based processing pipeline.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5471 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-18 19:25:15 +00:00
55e5971b3b
this is a oneoff script to clean the papuans and test TargetCreator and IndelRealigner with scatter gathering.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5457 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-17 17:09:53 +00:00
42f70d9e07
join all per-lane Bams before doing target realigning and indel cleaning.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5435 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-14 16:11:03 +00:00
0daa65b9ef
quick and dirty 'close your eyes' solution to run the papuans over the weekend. Will be properly fixed soon.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5370 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-03 21:42:22 +00:00
c7a51f0de7
fixed 1kg pilot dindel calls vcf file and combined all vcfs into one master dindel file.
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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
fd5d1f9cfc
minor cosmetic changes.
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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
81414a21dd
dpp: back to using 4gb memory assuming all is right with IndelRealigner now.
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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
6db3210387
the data processing pipeline needs more memory...
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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
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.
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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
2a48ec1307
now only accepts intervals files if the user specifically requests to report bams at interval only.
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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
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.
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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
d97ed3e080
Comments for Mauricio
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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
acad3ada06
changed baq to calculate_as_necessary.
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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
7f9ca6b28a
full data processing pipeline, now deleting intermediate files and performing both phases (per lane and combined) of the processing.
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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
497e9ab83b
too hasty... cleaning up debug messages ;)
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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
b4da843c49
now processes either a single bam file or a list of bam files in parallel.
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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
50c870cfce
Data Processing Pipeline: local indel realignment, mark duplicates and BQSR. Done.
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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
6d3b878dde
data processing pipeline script already does:
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. 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
87e19a17ae
small updates to the variant eval part of the pipeline, some updates to the pacbio specific pipeline.
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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
5f10fffa47
merge intervals now prints a sorted list in the end.
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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
50c2fa3c3a
this -1 made ALL the difference in the world. Minor bug fix.
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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
9c2c5efe35
a modified version of the Methods Development calling pipeline made to work with pacbio data.
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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
carneiro
depristo