Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Create VEP-compatible releases in CI #63

Open
holtgrewe opened this issue Nov 8, 2023 · 1 comment
Open

Create VEP-compatible releases in CI #63

holtgrewe opened this issue Nov 8, 2023 · 1 comment

Comments

@holtgrewe
Copy link
Contributor

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
Copy link
Contributor

davmlaw commented Nov 14, 2023

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

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants