I am attempting to reproduce a published analysis which, according to the authors, used MuTect 1.0.4. How might I acquire this (very) old version?
Check the source code repository -- the versions should be tagged, so you should be able to checkout the code, revert and build the version you want. Do you know how to use git?
Thanks for your response! I am not great with git but after trying a few things I see:
The oldest git version tag in the mutect repository is 1.1.4, however the log files go back much farther.
The oldest git version tag in the gatk repository is 1.0, but I am unsure of their correspondence to mutect.
Is there a way for me to figure out which version in either repository corresponds to mutect 1.0.4?
Ah, this makes me realize that MuTect was only moved to github late in development, so it's a no go on either repo I'm afraid. I'll have to check what we have in local archives. You can always ask the authors of that study to send you a copy of the jar they used, assuming they still have it.