[ensembl-dev] VEP fungi

[Will McLaren]

Dear Olivier,

Yes, it is possible to run VEP on any species in the Ensembl or Ensembl
Genomes collections. Downloadable cache datasets may not be available for
all species (someone in the e!Genomes team can clarify this), but you can
use the public database server in place, e.g.

perl variant_effect_predictor.pl -database -genomes -species
aspergillus_nidulans -i input.vcf [etc]

(-database tells VEP to use the database, -genomes is a shortcut providing
the e!Genomes public server details)

Regards

Will McLaren
Ensembl Variation

On 30 January 2015 at 13:12, Olivier Armant (ITG) <olivier.armant at kit.edu>
wrote:

> Dear Ensembl team,
>
> I have run succesfully VEP on mouse  and zebrafish dataset and would like
> now to try VEP on Aspergilus Nidulans.
> I do not manage to get the prebuild cache from ensembl fungi. Is it
> possible to run VEP on fungi at all? And if yes, could you direct me
> through the methodology?
>
> Best
>
> Olivier ARMANT
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