[ensembl-dev] regulatory_region_variant

[Graham Ritchie]

Hi Chris,

To get predictions for regulatory features you need the ensembl regulation API installed (the CVS repository is called ensembl-functgenomics for historical reasons) and you should supply the --regulatory command line option.

Cheers,

Graham


On 11 Nov 2011, at 08:47, cj5 at sanger.ac.uk wrote:

> Hi,
> According to the documentation, the ensembl api provides
> 'regulatory_region_variant' predicted variation consequences.
> 
> http://www.ensembl.org/info/docs/variation/index.html
> 
> But I've had a look at some of our annotations from the VEP 2.2, ensembl
> version 64, and not come across any instance of this. Is it not provided
> by the VEP?
> 
> I noticed a posting about this in the dev archives which suggests that
> since v62 we need to use VariationAdaptor for these annotation, but would
> like to check.
> 
> http://lists.ensembl.org/pipermail/dev/2011-May/001243.html
> 
> 
> Thanks
> Chris
> 
> 
> 
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