[ensembl-dev] VEP distance cutoff

[Genomeo Dev]

Hi,

Thanks for the response. For a given variant, I assume VEP looks at the
interval [-5KB, +5KB] and assigns as neighbours any genes which overlap
with that region. How are genes defined in this case? Does VEP look only
for overlapping TSS or the entire TSS<->TES region?

How about variants which are documented in the literature to occur in
enhancers which are say 1 MB from the target gene? Do these get taken into
account on top of the 5KB rule?

Thanks,

G.


On 5 February 2014 09:52, Genomeo Dev <genomeodev at gmail.com> wrote:

> Thanks very much.
>
> G.
>
>
> On 4 February 2014 22:02, Will McLaren <wm2 at ebi.ac.uk> wrote:
>
>> 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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>
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