[ensembl-dev] TSSDistance.pm does not take input structural variants in VEP

[Mike Pierce]

Hi,

Thanks Genomeo for bringing this up seems like an important issue. Ensembl
folks, could you please clarify whether Structural variants are processed
by the plugin by default or whether the variant_feature_types is required?

Cheers,

Mike


On 20 June 2014 18:25, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi Will/others,
>
> TSSDistance.pm currently does not seem to consider structural variants.
> Based on this doxygen documentation:
>
> public Listref
> Bio::EnsEMBL::Variation::Utils::BaseVepPlugin::variant_feature_types ()
>
>   Description: To indicate which types of variation features a plugin is interested
>                in, plugins should return a listref of the types of variation feature
>                they can deal with. Currently this list should include one or more of:
>                'VariationFeature' or 'StructuralVariationFeature'
>   Returntype : listref
>   Status     : Experimental
>
>
> I tried adding the following code at the top of the plugin:
>
> sub variant_feature_types {
>     return ['Variation','StructuralVariation'];
> }
>
> but it does not work.  This is the input in VCF:
> 5 104269332 CNV7 G <DEL> . PASS SVTYPE=DEL;END=104278677
>
> Any thoughts on that?
>
> Thanks,
>
> --
> G.
>
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