chapmanb/bcbio-nextgen — pull request #362 by mjafin (2014-03-19 14:59:02+00:00)
Title: Fixed downsampling in MuTect to match that of coverage_depth_max

Hi Brad,
I'm matching the downsampling coverage in MuTect to that specified in coverage_depth_max, otherwise MuTect downsamples to 1000 reads (default).

Also added some read filters that are already present in other Gatk tools.