approach to classify mutations

[alantsangmb]

Hello~ I have used clockwork to generate final.vcf files using the script only approach.
Any advises or tools I can adopt to further analyze the final.vcf files?
I would like to classify the mutations according to the WHO catalogue eventually.
Thanks in advance for your help.

[martinghunt]

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

Pinging @philipwfowler for advice...

[iqbal-lab]

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)

[philipwfowler]

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

[martinghunt]

Thanks @philipwfowler!

[alantsangmb]

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