GENCODE Primary annotation set

[dnil]

Description of feature

Ensembl recently plugged their reduced transcript set

https://www.ensembl.info/2025/02/14/cool-stuff-ensembl-vep-can-do-reduce-the-number-of-human-transcripts-you-need-to-consider-without-missing-results/

Still compatible with MANE and canonicals, but much reduced which would save both time and storage space: we have lots of duplication of the same noisy annotation for irrelevant transcripts, especially for SVs.

[jemten]

Thanks for bringing this to our attention! Sounds like we should go for this once we update ensembl version, the current validation is done with version 110.

[dnil]

Yeah, it appears a little limited still even on 113 - should be worth waiting for at least 114 for prod, but worth looking into given our dev cycles on lower-prio things. 😊