Ryan Poplin b22c9c2cb4 Improvements to the reference model pipeline. ... -- We use the RegenotypeVariants walker to recompute the qual field. (instead of the discussed idea of adding this functionality to CombineVariants) -- QualByDepth will now be recomputed even if the stratified contexts are missing. This greatly improves the QD estimate for this pipeline. Doesn't work for multi-allelics since the qual can't be recomputed.		2013-11-01 17:58:25 -04:00
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src	Improvements to the reference model pipeline.	2013-11-01 17:58:25 -04:00
test	Created a single sample calling pipeline which leverages the reference model calculation mode of the HaplotypeCaller	2013-09-06 16:56:34 -04:00