Support Appistry SomaticIndelDetector and bundle with calls to MuTect

Hi Brad,
Here are my proposed fixes for supporting SID without killing it for the Broad mutect release that doesn't contain SID. 

Feedback and constructive criticism very welcome :)

By the way, the Appistry mutect is called ```SomaticAnalysisTK.jar``` but I've symlinked it as muTect-1.1.6.jar if anyone ever asks how to get the Appistry version play nice with bcbio.