chartl 23fc9737b4 Added the ability to filter out variant (not truth) calls based on read depth. Using -NLD 5 will not update concordant counts for calls with 0, 1, 2, 3, or 4 reads supporting them. Not to be used with VCF files that do not have DP in the format field. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2716 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-27 23:28:04 +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	Ups, I did it again. Fixing the bug introduced in a previous commit: use correct length of the indel event.	2010-01-27 21:51:54 +00:00
oneoffprojects	Incremental update 2 -- refined allele and VariantContext classes; support for AttributedObject class; extensive testing for Allele class, and partial for VariantContext. Now possible to easily convert dbSNP to VariantContext.	2010-01-27 17:19:37 +00:00
playground	Added the ability to filter out variant (not truth) calls based on read depth. Using -NLD 5 will not update concordant counts for calls with 0, 1, 2, 3, or 4 reads supporting them. Not to be used with VCF files that do not have DP in the format field.	2010-01-27 23:28:04 +00:00
utils	Initial commit of v2.0 of the cleaner. DO NOT USE. (this means you, Chris)	2010-01-27 21:36:42 +00:00