Eric Banks b53336c2d0 Added hidden mode for BQSR to force all read groups to be the same one. ... * Very useful for debugging sample-specific issues * This argument got lost in the transition from BQSR v1 to v2 * Added unit test to cover this case		2013-05-06 19:09:10 -04:00
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haplotype	Address reviewer comments	2013-04-08 12:48:20 -04:00
haplotypeBAMWriter	Slightly improved Smith-Waterman parameter values for HaplotypeCaller Path comparisons	2013-04-11 18:22:55 -04:00
pairhmm	Quick optimization to the PairHMM	2013-04-14 23:25:33 -04:00
recalibration	Added hidden mode for BQSR to force all read groups to be the same one.	2013-05-06 19:09:10 -04:00