Feature request: Determine if there is a specific setting for annotating variant frequencies (gnomAD/gnomADg data) in the VEP API. - Githubissues

berntpopp / variant-linker

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Feature request: Determine if there is a specific setting for annotating variant frequencies (gnomAD/gnomADg data) in the VEP API. #10

Closed berntpopp closed 3 months ago

berntpopp commented 3 months ago

Current Behavior

It is unclear if there is a specific setting or option in the VEP API for annotating variant frequencies using gnomAD/gnomADg data.

Proposed Solution

Investigate the VEP API documentation and settings to identify any options for variant frequency annotations.
Test the identified settings to ensure they work as expected.
Document the findings and update the tool to utilize these settings if available.

Acceptance Criteria

[x] Identify and confirm any specific settings for variant frequency annotations in the VEP API.
[x] Implement the identified settings in the tool if applicable.
[x] Update the documentation to reflect the availability and usage of these settings.
[ ] Comprehensive tests are added to ensure variant frequency annotations are correctly handled.

berntpopp commented 3 months ago

Example: https://rest.ensembl.org/vep/human/region/16:3243310:3243310/G?content-type=application/json&mane=1&hgvs=1&merged=1 https://gnomad.broadinstitute.org/variant/16-3243310-A-G?dataset=gnomad_r4

The frequencies are automatically retrieved. There seems to be no specific setting in the endpoint documentation: https://rest.ensembl.org/documentation/info/vep_region_get

It is not clear form the VEP API DOcs which version is used

Potential future development: Implement dbNSFP annotations: https://raw.githubusercontent.com/ensembl-variation/VEP_plugins/main/dbNSFP.pm

Testing for variants will be implemented in #5 and #11