delangel be75b087ec a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype. ... b) Add "OG" annotation to genotypes. If Beagle changes genotypes, this annotation gets the original genotype call, to ease performance comparisons. If not, this annotation gets an empty value. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3723 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-06 18:33:28 +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	a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype.	2010-07-06 18:33:28 +00:00
test	part two: todo's in combine variants, fixes for InferredGeneticContext, and some other tests and clean-up.	2010-07-05 21:07:53 +00:00