chapmanb/bcbio-nextgen — pull request #52 by lbeltrame (2013-07-16 13:24:24+00:00)
Title: Add support for more snpEff options

I find myself using a lot the `-hgvs` option for snpEff as well as `-canon`. The former is used for HGVS style mutations (often used by clinicians, which I have to send my data to) and the latter to only use the canonical transcripts when evaluating annotations (something I use since I'm tracking mutations for targeted resequencing)

This proposal is here for review, in particular regarding the configuration options, currently put inside `algorithm` and their naming.