rpoplin eb07c7f7f8 CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2054 348d0f76-0448-11de-a6fe-93d51630548a		2009-11-16 18:44:54 +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/broadinstitute/sting	CountCovariates now warns the user if they didn't supply a dbSNP rod file. Thanks Kiran for the use case.	2009-11-16 18:44:54 +00:00
test/org/broadinstitute/sting	Stage 1 of the VariantFiltration refactoring is now complete. There now exists a parallel tool called VariantAnnotator which simply takes variant calls and annotates them with the same type of data that we used to use for filtering (e.g. DoC, allele balance). The output is a VCF with the INFO field appropriately annotated.	2009-11-16 02:41:20 +00:00