ebanks dc170caafc Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2678 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-25 17:27:12 +00:00
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alignment	Misc bug fixes.	2010-01-05 14:48:19 +00:00
analyzecovariates	Initial checkin of skeleton code for AnalyzeAnnotations	2010-01-15 21:52:34 +00:00
gatk	Now, if a dbsnp rod is passed to either the UnifiedGenotyper or VariantAnnotator, a DB=0/1 annotation is added (in addition to filling in the ID field); this is in line with 1KG project calls. If no dbsnp rod is used, the annotation is not added (as opposed to setting every entry to DB=0).	2010-01-25 17:27:12 +00:00
oneoffprojects	UG map() now returns a VariantCallContext object. Also has a field for confidentlyCalledBases. UG reduce() emits statistics on the confident called % of bases	2010-01-22 23:06:43 +00:00
playground	Don't reference that optimiation library I'm not using anyway.	2010-01-24 20:30:50 +00:00
utils	Better handling of enums by the command-line argument system.	2010-01-20 21:36:46 +00:00