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

Will McLaren wm2 at ebi.ac.uk
Mon Jun 23 13:50:33 BST 2014


Hi guys,

Thanks for finding this issue. I've had to patch a fix to the
ensembl-variation API module as it wasn't executing plugins correctly for
SVs.

A couple of further points:

The variant_feature_types() sub must get the name of the feature type e.g.
VariationFeature (not Variation). I have updated the TSSDistance plugin to
use the common base class BaseVariationFeature (both VariationFeature and
StructuralVariationFeature are child classes of this).

The plugin will not work for the variant you cite, since as explained in
the blurb at the top the plugin is for upstream variants only (though it
does work if you extend using UpDownDistance as I suspect you have been).
To modify it to work for downstream variants too you could remove the if{}
clause around the return statement and return the abs() value of $dist

Regards

Will McLaren
Ensembl Variation




On 23 June 2014 10:54, Mike Pierce <mikepierce2000 at gmail.com> wrote:

> 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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