search

SACGF / cdot

Transcript versions for HGVS libraries
MIT License
29 stars 5 forks source link

Create VEP-compatible releases in CI #63

Open holtgrewe opened 10 months ago

holtgrewe commented 10 months ago

I think that it would be feasible to run the VEP-compatible releases in CI.

The main limitation will be memory usage. A possible workaround may be using something like orjson for getting a potentially more memory efficient representation of the transcripts in memory.

davmlaw commented 10 months ago

We could just build and release everything

If you want to work out the appropriate GTF/GFF to get for a VEP release

Start with this VEP cache table

Eg for VEP 110

Annotation consortium Genome Build Location Version
Ensembl GRCh37 Last 37 Ensembl release - stuck version? 87
Ensembl GRCh38 Matches VEP release 110
RefSeq GRCh37 Listed under row "RefSeq" 2020-10-26 (GCF_000001405.25_GRCh37.p13_genomic.gff)  
RefSeq GRCh38 Listed under row "RefSeq" 110(GCF_000001405.40_GRCh38.p14_genomic.gff)  

Note: The dates don't match what's on RefSeq FTP site, may be a few days later