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rneher avatar rneher commented on July 30, 2024

Good idea! We will add a data set soon. What has been holding us back was the fact that clades are defined only for the HA gene. But we'll add NA data sets and can include tamiflu resistance mutations as 'labeled mutations'

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rneher avatar rneher commented on July 30, 2024

we have added NA datasets for A/H3N2, A/H1N1pdm, and B/Vic!

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jrotieno avatar jrotieno commented on July 30, 2024

Hi @rneher, Thank you for this implementation. I haven't spotted the 'labelled mutations" column when running nextclade H1N1 NA characterization. Is this in the pipeline or I am missing something?

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ivan-aksamentov avatar ivan-aksamentov commented on July 30, 2024

@jrotieno As far as I know this hasn't been done for flu datasets.

The split of mutations into labeled/unlabeled mutations requires some additional configuration in the dataset. The labels-to-mutations mapping and the reverse mapping, need to be precomputed (from the existing data) and then added into nucMutLabelMap and nucMutLabelMapReverse fields of the virus_properties.json file of the dataset. This is how it's configured in SARS-CoV-2:

I don't know if Richard and Cornelius plan to do this, but you can do this yourself too, by taking the existing virus_properties.json from a flu dataset ad adding these fields. Contributions are very welcome!

If you decide to try, in order to test things, you can override virus_properties.json in Nextclade CLI by using --input-virus-properties CLI parameter or in Nextclade Web by selecting a flu dataset, clicking "Customize dataset files" and dropping a file in the "Virus properties" section.

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