[ensembl-dev] VEP cache files for barley (Hordeum vulgare)

Will McLaren wm2 at ebi.ac.uk
Wed Nov 19 09:04:07 GMT 2014


By default when using --cache the VEP checks in with the DB server at
ensembldb.ensembl.org at the beginning of its run; barley is located on a
different server, which you can have the VEP connect to using --genomes

You can also bypass this connection completely by using --offline (with
limitations, see
though note in this case you must use the latin name for the species e.g.
--species hordeum_vulgare

In both the above cases you will also need to specify the e!Genomes cache
version using --cache_version 24, since the e!Genomes version numbers
differ from the main Ensembl version numbers (see

So, in summary, you can use either:

perl variant_effect_predictor.pl --cache --cache_version 24 --species
barley --genomes


perl variant_effect_predictor.pl --offline --cache_version 24 --species


Will McLaren
Ensembl Variation

On 18 November 2014 21:37, Fred Peng <fredyfpeng at ualberta.ca> wrote:

> Dear Developer,
> I am running VEP on barley (Hordeum vulgare L.) but could not make it
> work, with a message like: Hordeum_vulgare is not a valid species name
> (check DB and API version). I downloaded the cache file for barley
> hordeum_vulgare_vep_24_082214v1.tar.gz and unpacked it into ~/.vep
> directory. I run VEP with --cache option and specified --species
> Hordeum_vulgare.
> Any help (especially regarding cache file prep, how to specify a species
> -- common name or Latin name?) is appreciated.
> Cheers,
> Fred Peng
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