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

[Will McLaren]

Correct.

Will


On 24 June 2014 12:10, Mike Pierce <mikepierce2000 at gmail.com> wrote:

> 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.
>>>>
>>>
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>>
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>
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