bf2e02f472
Generic, easy-to-use variant evaluation Queue script that tests indel and SNP call sets against standard evaluation data sets for sensitivity and specificity
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5391 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-07 18:03:29 +00:00
8ab6eee1cf
gold standard creates its own tranches and vcf files now.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5347 348d0f76-0448-11de-a6fe-93d51630548a
2011-03-01 17:48:40 +00:00
ce34a8a918
New hidden option in VQSR to not parse the genotypes of the incoming training data. Updated VQSR training in methods development pipeline to be more in line with best practices.
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git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5340 348d0f76-0448-11de-a6fe-93d51630548a
2011-02-28 23:19:51 +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
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
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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
ecfb51bcd8
Few organizational changes, queue output is now categorized and hidden. Also changed NA12878.Wex to dbsnp 129.
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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
8ea71fd294
minor dataset chages.
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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
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
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
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
c630701a76
Following Ryan's suggestion, I am moving the Methods Development Calling pipeline to the Core.
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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
depristo
carneiro
rpoplin