I'm trying to build SomaticSpike, which is included in MuTect 1.1.4. Is there any way to actually build this from the github repository? Is there perhaps a binary floating around?
There's a binary of MuTect 1.1.7 available on the GATK downloads page, but I don't know if it includes this SomaticSpike thing -- that's the first I've heard of it.
SomaticSpike is only available in 1.1.4 and I can't find build instructions for that release. Is there an old binary? I'm actually not even sure if SomaticSpike is a different .jar. It's referenced in the original MuTect paper.
Sorry for the late response.
The source code for SomaticSpike is here:
However, it probably doesn't build on a recent version of GATK. You may be better off trying Bam Surgeon.