chapmanb/bcbio-nextgen — pull request #456 by mjafin (2014-06-17 10:35:37+00:00)
Title: Mutect: default to Scalpel instead of SID. Scalpel: use less stringent s...

...ettings for calling indels.

These updates improve sensitivity of Scalpel in NA12878 and the Dream challenge chr19 data without completely going overboard with FP. As SID is pants, I'd disable it from any future use from now until Broad update it.