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

[Will McLaren]

Hello,

Some variants are parsed by the VEP as structural variants, and these are
treated subtly differently as typically they are much larger than regular
sequence variants.

To enable your plugin to process both types, you should use:

return ['BaseVariationFeature'];

or for just structural variants

return ['StructuralVariationFeature'];

Regards

Will


On 9 May 2013 10:33, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  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> 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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>
>
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