[ensembl-dev] Annotations DBs

[Andrew Parton]

Hi Margaret,

VEP can provide annotations from three sources, which can be specified with a flag on VEP input:

—cache - Using a cache is the fastest and most efficient way to use VEP. With a cache file, the vast majority of annotations can be read from this file, reducing the number of required network connections. Cache files can be downloaded using the VEP installer, or can be downloaded manually if required. More information can be found on VEP caches here: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache <https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache>
—database - VEP can use remote or local database servers to retrieve annotations.  By default, VEP is configured to connect to the public Ensembl MySQL instance at ensembldb.ensembl.org. You can find more information on how to access our database servers, or to set up a local database here: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#database <https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#database>
—custom - If you have annotation data in a standard format such as GFF, VCF or BED, you can integrate this data into your VEP output using our custom annotation functionality. For more information on custom annotations, please see https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html <https://www.ensembl.org/info/docs/tools/vep/script/vep_custom.html>

Let us know if there’s anything else we can do to help.

Kind Regards,
Andrew

> On 10 Mar 2020, at 00:40, Linan, Margaret <margaret.linan at mssm.edu> wrote:
> 
> Hi – 
>  
> How do you get the annotations dbs for VEP? I know I can specify them on the command line but they did not come with my installation.
>  
> Thanks,
> Margaret
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