Attention: Want an end-to-end pipelining solution for GATK Best Practices?
differences between 3 versions of MuTect
I've been running 3 different versions of MuTect on a set of tumor and matched-normal samples. Although all three versions produce comparable counts of somatic mutations, only the pre-release version (muTect-1.0.27783) returns anything with the 'KEEP' status. The other 2 versions ( muTect-1.1.1 and muTect-1.1.4) reject ALL returned somatic variants. I'm running all 3 versions of the software with default parameters. I was wondering if you could tell me what's different between the 3 releases of MuTect and why the later versions seem to be more conservative.