depristo b8d6a95e7a Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3690 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-30 20:13:03 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org	Preliminary commit of new VCFCombine, soon to be called CombineVariants (next commit) that support merging any number of VCF files via a general VC merge routine that support prioritization and merging of samples! It's now possible to merge the pilot1/2/3 call sets into a single (monster) VCF taking genotypes from pilot2, then pilot3, then pilot1 as needed.	2010-06-30 20:13:03 +00:00
test/org/broadinstitute/sting	Refactored and generalized the database/comp annotations in VariantAnnotator. Now one can provide comp tracks as with VariantEval (e.g. compHapMap, comp1KG_CEU) and the INFO field will be annotated with the track name (without the 'comp') if the variant record overlaps a comp site (e.g. ...;1KG_CEU;...). This means that you can now pass 1kg calls to the Unified Genotyper and automatically have records annotated with their presence in 1kg.	2010-06-30 16:37:31 +00:00