gatk-3.8

Author	SHA1	Message	Date
jmaguire	65a788f18a	Added a ROD (SangerSNP) for parsing the Sanger's chr20 pilot1 SNP calls. Some doodling around with indel calling in an EM context. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1116 348d0f76-0448-11de-a6fe-93d51630548a	2009-06-29 16:32:12 +00:00
depristo	819862e04e	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	2009-06-05 23:34:37 +00:00
depristo	ce6a0f522b	First incarnation of the population-based SNP analysis tool. Also bug fixes throughout the GATK git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@845 348d0f76-0448-11de-a6fe-93d51630548a	2009-05-27 22:02:24 +00:00