I'm using MuTect2 to call variants. The output vcf is in 4.2 format. I was wondering if there's a way to configure MuTect2 to use vcf 4.1 format instead?
I know there was an option to do the opposite of what you are asking! I'm not sure if there is an option to do what you want, but I will ask the team.
I'm afraid that's not possible, sorry. You can try to "fake it" by manually editing the version number in the VCF header, but if you try to feed the file to any downstream software that doesn't support 4.2, there's a chance it will break. We find that the best thing to do is ask the authors of the software to upgrade their code to support the newer format.