Enhancement: Add the ability to specify the genome build reference (hg19/hg38) for annotations in the Variant-Linker tool. - Githubissues

berntpopp / variant-linker

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Enhancement: Add the ability to specify the genome build reference (hg19/hg38) for annotations in the Variant-Linker tool. #9

Open berntpopp opened 2 weeks ago

berntpopp commented 2 weeks ago

Current Behavior

Currently, the tool uses the hg38 endpoint for annotations, and all annotations are thus based on the hg38 build.

Proposed Solution

Investigate and confirm the current usage of the hg38 endpoint.
Update the documentation to reflect the current behavior.
Add an option for users to specify the genome build (hg19 or hg38).

Acceptance Criteria

[x] Confirm the current usage of the hg38 endpoint for annotations.
[ ] Update the documentation to specify that the tool currently uses the hg38 build.
[ ] Implement an option for users to specify the genome build (hg19/hg38).
[ ] Comprehensive tests are added to verify correct handling of both genome builds.

berntpopp commented 2 weeks ago

The endpoint used (https://rest.ensembl.org/documentation/info/vep_region_get) currently only supports assembly_name "GRCh38".

To implement "grch37" we wold need to add an option/ parameter and then use the legacy endpoint https://grch37.rest.ensembl.org/documentation/info/vep_region_get.

For implementation insure compatability and that additional options are supported.