iqbal-lab-org
approach to classify mutations
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.
Interpreting the VCFs/catalogues is beyond the scope of Clockwork, which makes the variant calls.
Pinging @philipwfowler for advice...
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)
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
