Implements a new category based on the PM5 ACMG criteria
Closes #140
Proposed Changes
Includes a helper script with code used to take a clinvar VCF annotated by VEP, reshuffle the content into a Hail Table linking all Protein_ID and residue number with all relevant clinvar alleles
This helper isn't being built up into a proper wrapper script because once VEP is released on Hail Query that will be much easier to develop. Pretty manual until then
Includes a categorydetailspm5 which will collect all clinvar missense submissions at the same residue as a current missense
any matched submissions that are an exact match to this current variant are removed
This data is processed to create a new column in the report HTML with hyperlinks to the other entries (if appropriate)
needs further testing, but happy to force this through for now to freeze functional code - happy to increase test coverage
Waiting for tweaks to downgrade the pm5 from being a full category to being a type of support
Fixes
Proposed Changes
categorydetailspm5
which will collect all clinvar missense submissions at the same residue as a current missenseWaiting for tweaks to downgrade the pm5 from being a full category to being a type of support
Checklist