[ensembl-dev] VEP output with regulatory feature & conservation plugin

[Will McLaren]

Hi Guillermo,

The feature_types sub determines when the plugin is run depending on what
feature type the TranscriptVariationAllele object overlaps.

To enable your plugin to run on every variant, regardless of what it
overlaps, you should have the sub return:

return ['Feature','Intergenic'];

Remove 'Intergenic' if you don't want the plugin to run on variants that
don't overlap a transcript or regulatory feature.

'Feature' is a catch-all type that includes transcripts and regulatory
feature types.

Hope this helps

Will


On 9 May 2013 08:11, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hello,
>
> While I'm using VEP flag "--regulatory" flag I notice a weird output in my
> vep file.
> Some lines present all empty columns except: Consequence, Feature and
> Feature_type.
>
> While I'm using VEP plugin Conservation (available in VEP github
> repository) some lines present all empty columns except: Consequence,
> Feature, Feature_type and Conservation.
>
> I would like that the rest of my columns (obtained from VCF through
> plugin) are also show. I think this has something to do with the following
> lines in my plugin:
>
> sub feature_types {
>
>     return ['Transcript'];
>
> }
>
>
> I'm am wrong?
>
> Thank you !
>
> Best regards,
> Guillermo.
>
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