chapmanb/bcbio-nextgen — pull request #59 by lbeltrame (2013-07-19 08:24:55+00:00)
Title: Initial implementation of MuTect tests

Like when I started with the actual thing, this patch is *incomplete* and needs review.

It misses a proper data file and there are some design decisions to take: personally I'd use already-made BAMs, if available, since we're only interested in the results from the variant calling, but I'm open to suggestions.

The test is marked as expected failure (using a decorator I added) until the open questions are addressed.