approach to classify mutations about clockwork HOT 5 OPEN

Interpreting the VCFs/catalogues is beyond the scope of Clockwork, which makes the variant calls.

Pinging @philipwfowler for advice...

from clockwork.

The WHO catalogue is not really in a fit state for bioinformatic processing (or wasn't on release, i havent checked the latest update), so it is non trivial to go from VCF+WHO to results. Phil is on top of this though (cc-ed above). We did add WHO support to Mykrobe though, for what that is worth (https://github.com/Mykrobe-tools/mykrobe/releases)

from clockwork.

Yes we've written a tool that consumes a Clockwork vcf, a catalogue and a genbank file. It builds on other tools we've written and we've also translated the WHO catalogue into a form that we can parse. https://github.com/oxfordmmm/gnomonicus

from clockwork.

Thanks @philipwfowler!

from clockwork.

Thank you all!
I will look into Mykrobe and gnononicus.

from clockwork.