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iqbal-lab-org / clockwork

CRyPTIC data processing pipelines
MIT License
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approach to classify mutations #104

Open alantsangmb opened 1 year ago

alantsangmb commented 1 year ago

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 commented 1 year ago

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

Pinging @philipwfowler for advice...

iqbal-lab commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Thanks @philipwfowler!

alantsangmb commented 1 year ago

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