chapmanb/bcbio-nextgen — pull request #392 by mjafin (2014-04-08 10:53:15+00:00)
Title: Added configurable min-alternate-fraction to FreeBayes

Hi Guys,
I added the configurable minimum AF option into FreeBayes based on Brad's backend work. Defaults to 20 (FreeBayes default) in both single and paired end calling, happy to change these.

In addition, I think it would be nice if FreeBayes didn't die in case singleton tumor samples were given to it. I think it could just revert to single sample mode or something.. opinions anyone? This would be practical in case of combining variant calling across methods, where MuTect supports single sample tumors (but not single sample normals).