Ryan Poplin d978cfe835 Soft clipped bases shouldn't be counted in the delocalized BQSR.		2012-11-25 21:55:29 -05:00
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bqsr	Soft clipped bases shouldn't be counted in the delocalized BQSR.	2012-11-25 21:55:29 -05:00
compression/reducereads	Refactored the BaseCounts classes so that they are safer and allow for calculations on the most probable base (which is not necessarily the most common base).	2012-10-04 10:37:11 -04:00
genotyper	Moving UG integration tests to protected since they use protected-only contamination filtering. Adding a new UGLite integration test to confirm that contamination filtering is ignored in lite.	2012-10-31 21:28:07 -04:00
haplotypecaller	The default value for --contamination_fraction_to_filter is now 0.05 (5%) in both UG and HC. Users of GATK-lite get pushed down to 0% by default (since it's not enabled) or get a user error if they try to set it.	2012-10-26 01:04:51 -04:00