Since moving back to pulling Pedigree data from Metamist we have a bug where we try to test MOI using participants not in the joint call
Proposed Changes
Retain snRNA transcript consequences
Allow snRNA variants in de novo testing
Fix hyperlinks
allow for missing family members when testing MOI
Notes
Since this change ClinvArbitration will be calling variants Pathogenic/Likely Pathogenic, instead of just Pathogenic. Looking at the code here we don't need to adjust to this change. We're testing for clinvar_significance.lower().contains('pathogenic') which will still be true.
Now that we're using ClinvArbitration we no longer have "conflicting interpretations of pathogenicity", which was a conflating status, and meant we had to test for "contains pathogenic, and doesn't contain conflicting", so that's been simplified.
Fixes
Proposed Changes
Notes
Since this change ClinvArbitration will be calling variants
Pathogenic/Likely Pathogenic, instead of justPathogenic. Looking at the code here we don't need to adjust to this change. We're testing forclinvar_significance.lower().contains('pathogenic')which will still be true.Now that we're using ClinvArbitration we no longer have "conflicting interpretations of pathogenicity", which was a conflating status, and meant we had to test for "contains pathogenic, and doesn't contain conflicting", so that's been simplified.
Checklist