Get mutations from BN and identify resistance

folkehelseinstituttet / SC2_drug_resistance

Analysis of Sars-Cov-2 drug resistance mutations from the Stanford database

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Open jonbra opened 7 months ago

jonbra commented 7 months ago

Pros: The analysis is automatically executed every time a new sample is analysed.

Cons: May require a lot of extra work just to implement in the routine. Difficult to re-run or update if new resistance mutations/data is released.

jonbra commented 7 months ago

Simply create lists of mutations in NSP5, with Stanford-compatible numbering.

Match these against the stanford mutations.

jonbra commented 7 months ago

[ ] Read the ORF1a (nsp5) and PRF1b (nsp12) mutations directly from BN
[ ] Convert these mutations to Stanford nomenclature (already have code for) and and store these in separate columns for nsp5 and nsp12.
[ ] Match the nsp5 and nsp12 columns with the resistance mutations provided by Stanford (see #2).