Mauricio Carneiro 5af373a3a1 BQSR with indels integrated! ... * added support to base before deletion in the pileup * refactored covariates to operate on mismatches, insertions and deletions at the same time * all code is in private so original BQSR is still working as usual in public * outputs a molten CSV with mismatches, insertions and deletions, time to play! * barely tested, passes my very simple tests... haven't tested edge cases.		2012-02-09 18:46:45 -05:00
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broadinstitute/sting	BQSR with indels integrated!	2012-02-09 18:46:45 -05:00