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

Mike Pierce mikepierce2000 at gmail.com
Tue Jun 24 12:10:29 BST 2014


Thanks Will. I suppose UpDownDistance.pm considers  upstream and downstream
distances respectively from the start and the end of the SV. Is that right?

Cheers,

Mike


On 23 June 2014 13:50, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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.
>>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
>>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140624/c940062f/attachment.html>


More information about the Dev mailing list