[ensembl-dev] VEP distance cutoff

[Will McLaren]

Hello,

The VEP looks at +/- 5KB either side of each transcript's start and end
coordinates; these coordinates are inclusive of any UTR regions. A gene is
defined by the furthest-reaching 5' and 3' coordinates of the transcripts
in that gene. You might find the diagram on this page useful:

http://www.ensembl.org/info/genome/variation/predicted_data.html#consequences

The VEP separately annotates regulatory regions (in human and mouse at
least) as determined by the Ensembl regulatory build; to enable this just
add --regulatory to your VEP command.

http://www.ensembl.org/info/genome/funcgen/regulatory_build.html

http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_regulatory

Regards

Will McLaren
Ensembl Variation


On 17 February 2014 10:04, Genomeo Dev <genomeodev at gmail.com> wrote:

> 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
>>>>
>>>>
>>>> _______________________________________________
>>>> Dev mailing list    Dev at ensembl.org
>>>> Posting guidelines and subscribe/unsubscribe info:
>>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>> Ensembl Blog: http://www.ensembl.info/
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Dev mailing list    Dev at ensembl.org
>>> Posting guidelines and subscribe/unsubscribe info:
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>> Ensembl Blog: http://www.ensembl.info/
>>>
>>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140217/7517fff3/attachment.html>