LegacyVariation or VRS?

[mshadbolt]

Quick question re: genomicVariants, does the Beacon team recommend following the VRS variant specification (i.e. either MolecularVariation or SystemicVariation) for defining the variation field in genomicVariant objects or are you agnostic to which reference is used?

I am not sure whether the LegacyVariation definition is something to ensure backward compatibility only and it is preferred to use the VRS schemas for any new beacons or it is still a valid option moving forward?

[mbaudis]

@mshadbolt Good question. We probably should be more empathic about using VRS - however, this had been a bit of a moving target during late development/approval of Beacon v2, therefore the half-hearted implementation & documentation. The "legacy" part (e.g. "variantType": "SNP", "alternateBases": "A" ...) was primarily as an offer to implementers who may not yet be on the VRS track (i.e. most) to provide a soft landing.

IMO we should emphasize VRS format (in fact the location part of the "legacy" type also uses VRS locations). It would be great if you could e.g. PR some examples here https://github.com/ga4gh-beacon/beacon-v2/tree/main/models/src/beacon-v2-default-model/genomicVariations/examples !

[mshadbolt]

Ok great, thanks @mbaudis , thanks for confirming. It makes sense to me that the VRS approach would be favoured moving forward.

Our group is working on generating some examples for our own purposes so will definitely add some examples via a PR when I have generated some.

[mbaudis]

@mshadbolt WDYT about moving to a more VRS vocabulary in queries, e.g. alternateBases => sequence, ditching referenceBases and assemblyId ... etc.? I'm interested in getting users' opinions (I'm in favour).