[ensembl-dev] VEP Extra output information

[Guillermo Marco Puche]

Hello,

I'm looking for an example *.vcf output with ALL the "Extra" parameters.
I've generated some with VEP script but i'm missing some extras never 
being generated like HGNC.

A few lines VCF with all values would be enough, since i'm planning to 
parse "Extra" column.

It also would be great if it includes most of the plugins outputs also :)

Thank you :)

Best regards,
Guillermo.

On 04/16/13 18:00, Guillermo Marco Puche wrote:
> On 04/16/13 14:49, Will McLaren wrote:
>> 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.
> Since additional data is being obtained from multiple sources, APIs, 
> files, etc.. I guess plugins are the only way to go for me.
>> 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.
> Where are packages likepackage Conservation; comming from?
>> 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).
> I'll look further into this tomorrow since I've to go now.
>
> A workaround could be simply generating a temp file with extra columns 
> and in the end merge original VCF from VEP script with the output from 
> plugins for additional columns.
>
> Maybe I missunderstood you. Correct me if i'm wrong please.
>> Hope this helps, and feel free to ask further questions!
>>
>> Will McLaren
>> Ensembl Variation
> Thank you so much.
>
> Best regards,
> Guillermo.
>> 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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>
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