chapmanb/bcbio-nextgen — pull request #40 by cswegger (2013-07-08 07:43:35+00:00)
Title: Initial support for the MuTect tumor/normal calling algorithm

*Warning*: This patch is *incomplete*! It will *not* work. It's probably very ugly as well.

The reason this is being posted is for:

* Code review
* Discussion of the implementation
* Discussion on the design
* Discussion of possible challenges.

Given the fact that MuTect is a modified GATK, I thought the best option would be to integrate it in BroadRunner. However I'm not sure on how to specifiy the MuTect jar correctly. I also have checked the MuTect syntax and unfortunately it requires *two* different BAMs to operate, but said BAMs need to be realigned together (if using the GATK best practices) to compensate for slight differences between tumor and normal.

Metadata should be used to identify tumor and normal.

Some possible solutions:

* Split BAMs, save in the work directory, pass to the algorithm.
* Get the merged BAM, split in a temporary directory, then run the algorithm from the files (ugly, that's what I do at the moment in my own scripts).

Currently I assumed that the order of BAMs in the list is defined, but likely it is not.
There are a lot of issues in the code and the work is not done, but I prefer starting off a clean design than to build a hack, that's why I'm posting it now.

TODO: handle the variant calling from the algorithm.