cancervariants / cancervariants/variation-normalization

Add support for transcript variant normalization

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#632 1 comment 0 reactions 0 assignees View on GitHub
enhancement
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

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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

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