Show nearby SNV assessments
Background
It is useful for users to see nearby allele assessments (e.g. BRCA1 NM_000059.3:c.123A>G 2021-05-03 Class 5
) when they are evaulating a variant (e.g. NM_000059.3:c.124T>C).
See associated epic for how this can be extended in the future. The current issue serves as a starting point to get most of the framework in place.
Implementation
- Add an endpoint of the form
api/v1/workflows/analyses/<int:analysis_id>/similar?allele_ids=1,2,3
, and return a JSON of variants that are similar to the provided allele ids. - Call endpoint from frontend and add results Cerebral state tree
- Add a section in the interpretation view (below
Classification
, aboveFrequency
) named "Similar variants" - see mockup below.
UPDATE 14.06.2021: User feedback suggests naming section "Region" instead of "Similar variants"
UPDATE 24.06.2021: Change from "Variants within 100 bp" to "Variants +/- 100 bp (first 10)" (where 10 =max_variants
) - Add config values for e.g.
max_variants_returned
andmax_genomic_distance
inexample_config.yml
UI mockup
Note: For the variant, these should be given, if possible:
- Gene
- HGVSc (short/no transcript ref, like in the sidebar)
- HGVSp (short/no protein ref; show in "()")
- Existing class
- Date of last interpretation
Considerations
VarDB contains a lot of variants that are normally filtered and therefore never get a classification. These variants are not interesting to the interpreter, unless they are within the same sample/analysis (and generate the Another variant warning). Can results be limited to variants that have a classification or are within the same analysis only?
TODO: Add endpoint for allele workflow as well