chapmanb/bcbio-nextgen — pull request #446 by lbeltrame (2014-06-09 08:29:11+00:00)
Title: Add REJECT filter to non-somatic records in VarScan2

Like the work done in FreeBayes, this patch adds a REJECT filter to
non-somatic records (i.e., everything with a Somatic Status - SS - not
equal to 2) produced by VarScan2.

It includes some duplicated code from FreeBayes, which could be moved to
vcfutils.

As usual this is a WIP! I'll be unable to test this in the coming days, so additional testing is welcome.