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

[Genomeo Dev]

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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