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monarch-initiative / genophenocorr

Genotype Phenotype Correlation
https://monarch-initiative.github.io/genophenocorr/stable
MIT License
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Support mapping an HGVS annotation to `VariantCoordinates` #75

Closed ielis closed 8 months ago

ielis commented 9 months ago

Add stubs for mapping an HGVS annotation to VariantCoordinate using Ensembl's REST API.

We must implement genophenocorr.preprocessing._vep.VepHgvsVariantCoordinateFinder stub and make the associated unit tests pass.

See the stub for more information/guidance.

Closes #76 Resolves BIH-CEI/ERKER2Phenopackets/#178

ielis commented 9 months ago

We can also use variantvalidator.org REST API; this may be even better since it directly serves VCF coordinates, which are straightforward to translate into VariantCoordinates:

E.g. for NM_005912.3:c.253A>G:

curl -X 'GET' \
  'https://rest.variantvalidator.org/VariantValidator/variantvalidator/hg38/NM_005912.3%3Ac.253A%3EG/mane_select?content-type=application%2Fjson' \
  -H 'accept: application/json'