[ensembl-dev] VEP Extra output information

Will McLaren wm2 at ebi.ac.uk
Tue Apr 16 13:49:52 BST 2013


Hi Guillermo,

There's two distinct ways you can add additional data to the output
from the VEP.

1) Custom annotations - here you simply provide the VEP with a
tabix-indexed position-based data file, and the VEP does the work of
finding overlaps with your variant input and the data from the file.

2) Plugins - you write the code to add to or manipulate the internal
data structures used by the VEP. In its simplest form, a plugin can be
simply looking up an attribute of some object and adding it to the
output.

Writing a plugin requires a basic understanding of the Ensembl API,
but getting a basic plugin working requires only a very small amount
of code.

The documentation
(http://www.ensembl.org/info/docs/variation/vep/vep_script.html#plugins)
explains all of this, but the best way to see how plugins work is to
look at the existing plugins at
https://github.com/ensembl-variation/VEP_plugins. I'd suggest looking
at Conservation.pm and ProteinSeqs.pm as some relatively simple
examples of retrieving additional data from the API.

You should note that using VCF output you will see repeated elements
in the INFO field added, since the plugin gets run once for every
variant/transcript overlap; all data appear under the CSQ field in the
INFO column. Currently there is no way for the VEP via plugins to add
separate INFO fields, however this is something we are looking into,
and in fact would be relatively easy to "hack" in for someone
determined enough (see subroutine vf_list_to_cons in
Bio::EnsEMBL::Variation::Utils::VEP).

Hope this helps, and feel free to ask further questions!

Will McLaren
Ensembl Variation

On 16 April 2013 12:58, Guillermo Marco Puche
<guillermo.marco at sistemasgenomicos.com> wrote:
> Hello,
>
> I'm in need to develop some extra features for VEP.
>
> My input files are in VCF format and also my output.
>
> But I want to add several additional columns for extra data at the VCF out.
>
> For example,AA conservation score, Biobase description, Biobase link, MAF
> populations, Flanking sequence, Gene description, InterPro_ID and more..
>
> I've been reading the documents and I'm a bit confused about "Custom
> annotations".
> I think since the data I want is extra on the output and not in the input,
> what I should do is develop several Plugins to obtain all the values I need.
>
> I think most of them can be obtained through the Ensembl API even if I'm new
> to this. Other will require more hard coding.
>
> I hope someone can clarify me a bit on this matter.
>
> Thank you.
>
> Best regards,
> Guillermo.
>
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