[ensembl-dev] VEP distance cutoff

[Genomeo Dev]

Thanks.

With regard to --regulatory option, Having run VEP with 1000G variants
using this option I found that, in the output, whenever a variant is
predicted to have a Feature type: RegulatoryFeature or MotifFeature, there
is no entry in the GENE or SYMBOL columns and also unlike for variants with
Feature type Transcript, CELL_TYPE is populated.

Is this a reflection of the fact that current data in the
Ensembl regulatory build are (1) cell-type specific (2) genome-wide
profiling experiments which don't associate regulatory regions to the
actual genes whose expression is being regulated?

Thanks,

G.





On 17 February 2014 10:18, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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
>>>>>
>>>>>
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>>
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>
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