cancervariants / cancervariants/variation-normalization
Frameshift variants should not return valid VRS objects in gnomad_vcf_to_protein
- Dominant language
- Python
- Stars
- 15
- Forks
- 2
- PR merge metrics
- No merged PRs in 30d
Description
### Describe the bug
VRS does not currently support variants where there is a resulting frameshift. We should detect this and return an error. Currently, we return incorrect VRS objects in cases of frameshifts
### Steps to reproduce
1. Attempt to normalize vcf coords that are known to result in a frameshift in the /gnomad_vcf_to_protein endpoint (ex: 17-43124028-CTCT-CT)
2. notice that there is a VRS object returned
### Expected behavior
We should not return a VRS Allele since VRS does not support fs variants currently. We should return a warning saying "Frameshift variants are currently not supported" or something of that sort
### Current behavior
valid vrs allele returned
### Possible reason(s)
we don't check for it
### Suggested fix
check for if a variant results in a frameshift before converting/returning
### Branch, commit, and/or version
any
### Screenshots
_No response_
### Environment details
Not applicable
### Additional details
:)
### Contribution
None
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by reproducing the /gnomad_vcf_to_protein request with 17-43124028-CTCT-CT and trace the endpoint's variant conversion path. Confirm that frameshift results produce a warning such as "Frameshift variants are currently not supported" and no VRS Allele, then run the relevant endpoint tests if available.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- api, bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100