cancervariants / cancervariants/variation-normalization
Add support for transcript variant normalization
- Dominant language
- Python
- Stars
- 15
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
### Feature description
In our clinical variation landscape paper, we reportedly do not normalize c. ranged variants such as "VHL A56_P59del (c.166_178del)" because a genomic coordinate is not provided, but this is actually very achievable using UTA.
I think we should add support for this feature.
### Use case
N/A
### Proposed solution
_No response_
### Alternatives considered
_No response_
### Implementation details
_No response_
### Potential Impact
_No response_
### Additional context
_No response_
### Contribution
None
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reviewing the existing normalization entry points for transcript variants and how they use UTA, since the issue names no files or tests. Determine the intended behavior for c.-ranged variants such as VHL A56_P59del (c.166_178del), then define tests that establish when normalization is complete.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- backend
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100