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

Guillermo Marco Puche guillermo.marco at sistemasgenomicos.com
Thu May 9 10:33:56 BST 2013


Hello,

Ok this seems to clarify all.

What about plugins with also variant_feature_types sub-routine?

sub variant_feature_types {
     return ['VariationFeature'];
}

Thank you.

Best regards,
Guillermo.

On 05/09/2013 10:19 AM, Will McLaren wrote:
> 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 
> <mailto: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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