Include var-pt-map.py? - Githubissues

TYTYBU / vcfByGene

Parse and filter UKB vcf files by gene

BSD 3-Clause "New" or "Revised" License

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Include var-pt-map.py? #2

Open sean-at-biohaven opened 1 month ago

sean-at-biohaven commented 1 month ago

The README.md mentions the script var-pt-map.py, but I can't find this script in the repository. I'm very interested in it, if you're able to share it alongside the Jupyter notebooks you've already provided!

TYTYBU commented 1 month ago

Sorry the original scripts were store on our DNAnexus project folder. I have just updated the repo to include these. Hope it helps!

sean-at-biohaven commented 1 month ago

Thank you very much for your rapid response @TYTYBU ! Can you please explain the -v parameter to this script (annotated variant file)? Are these files output from the VEP step as explained in the README.md?

Also, if I don't care about the severity of the variants, is it possible to skip the annotation step?