Is there somewhere I can get the muTect 1.1.6 jar file or do I need to compile?
@datakid Try https://github.com/broadinstitute/mutect/releases. Also, we have MuTect2, albeit in beta, available with the GATK jar.
We do provide a precompiled MuTect 1.1.7 jar file on our downloads page. I don't think 1.1.6 is available pre-compiled anywhere; 1.1.5 was the last pre-compiled release.