[ensembl-dev] VEP distance cutoff

Will McLaren wm2 at ebi.ac.uk
Tue Feb 4 22:02:59 GMT 2014


Hello,

The default cutoff is 5000 bases.

There is no parameter in the VEP itself, but there is a plugin available
that can be used to change the parameter.

https://github.com/ensembl-variation/VEP_plugins/blob/master/UpDownDistance.pm

http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html

Regards

Will McLaren
Ensembl Variation


On 4 February 2014 17:48, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> Using VEP in Ensembl VM v74
>
> 1. I was wondering what distance cutoff does VEP use to assign
> neighbouring genes to input variants.
> 2. Is there a parameter to handle that?
>
> Thanks,
>
> Genomeo
>
>
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