populationgenomics / talos

Rare Disease variant reanalysis tool
MIT License
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Proposal: AlphaMissense Ascendant #370

Closed MattWellie closed 7 months ago

MattWellie commented 7 months ago

Re-work the categories to adjust to the facts:

Proposed changes

  1. Replace the CADD/REVEL involvement in Cat. 2 with AM pathogenicity
  2. Remove the CategorySupport logic. The code placeholders to trigger 'support' logic will remain, but we just won't exercise those for now.
  3. Add back-filtering logic to remove variants after MOI application where they are Cat6 only, and the variant-gene has not been phenotype-matched to this participant

Future

MattWellie commented 7 months ago

As a prototype I'm going to leave the possibility of a Cat6-only compound het pair without phenotype matching. The logic to remove those will be fiddly, and might only affect a tiny number of variants