depristo
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84d407ff3f
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Fixing odd merge problem with VariantEval -- better cluster analysis (no cumsum), rodVariant is now an AllelicVariant
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1239 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-14 18:53:27 +00:00 |
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depristo
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f5b00c20d0
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Updated python files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1182 348d0f76-0448-11de-a6fe-93d51630548a
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2009-07-07 14:15:39 +00:00 |
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depristo
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5289230eb8
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Version 0.2.1 (released) of the TableRecalibrator
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1108 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-25 22:50:55 +00:00 |
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depristo
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8ac40e8e2d
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Updated version of the recalibration tool
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1060 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-19 17:45:47 +00:00 |
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depristo
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1fb241a8b8
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Now supports resume and dry runningRecalQual.py
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@996 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-11 23:31:59 +00:00 |
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depristo
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7fa84ea157
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10x speedup of recalibration walker
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@954 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-09 15:39:40 +00:00 |
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depristo
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819862e04e
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major restructuring of generalized variant analysis framework. Now trivally easy to add additional analyses. Easy partitioning of all analyses by features, such as singleton status. Now has transition/transversional bias, counting, dbSNP coverage, HWE violation, selecting of variants by presence/absense in dbs. Also restructured the ROD system to make it easier to add tracks. Also, added the interval track -- if you provide an interval list, then the system autoatmically makese this available to you as a bound rod -- you can always find out where you are in the interval at every site. Python scripts improved to handle more merging, etc, into population snps.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@918 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-05 23:34:37 +00:00 |
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depristo
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67112c79a1
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More robust individual genotypes to population script
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@893 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-04 00:12:31 +00:00 |
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depristo
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3998085e4b
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more and better python scripts for dealing with calls
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@881 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-02 20:37:19 +00:00 |
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depristo
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ae2eddec2d
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Improving, yet again, the merging of bam files
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@874 348d0f76-0448-11de-a6fe-93d51630548a
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2009-06-02 13:31:12 +00:00 |
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depristo
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543c68cdd8
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First version of individual geli files to population SNPS
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@865 348d0f76-0448-11de-a6fe-93d51630548a
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2009-05-31 15:29:10 +00:00 |