Maybe Cancer Genome Interpreter would be handy in this scenario? Not sure what is the plan (or if that is what we actually need to discuss) but I used this quite often when working on a breast cancer personalised medicine program. Has an API or you can download the full set and use it to annotate your mutations and classify them according to oncogenicity. This is of course focused on cancer, not sure if we will try to cover other things.

Do they have documentation and executables on GitHub? I only found the web tool and FAQ page.

Mmm I think that is all they have, cancer genome interpreter is a annotation tool that only works connecting to their database at the moment. Under the hood they are using their algorithms that are in independent papers (boostdm and oncodriveMUT). The API normally works quite well, very few times I have had issues and when I wrote to them they solved it within a day

we also have a cl tool on pypi that is capable of accessing the CGI KB for VCFs: https://pypi.org/project/querynator/ A problem might be that for running many files the CGI API only allows 2 jobs in parallel

@Raquel Manzano Thanks a lot. I will definitely try to use CGI and test it out locally!

Great, feel free to message me if you need any help