[ensembl-dev] Variant/Phenotype assocation plugin: How to output annotation per consequence correctly?

[Will McLaren]

Hi Guillermo,

For the ClinVar data Ensembl doesn't import the RefSeq reported, only the
associated gene symbol. This along with other data are available in the
attributes of the phenotype feature object ($pf->get_all_attributes).

Regards

Will McLaren
Ensembl Variation


On 17 June 2016 at 12:29, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

> Dear devs,
>
> I've been using this plugin I made with the help of Will McLaren:
> https://gist.github.com/guillermomarco/be0751f77b798d37ded14e5a884e4ff0
> I'm pretty happy with the results however I would like to improve it. At
> this moment plugin outputs the selected phenotypes for all the consequences
> per transcript. However this is not right.
>
> If I annotate the following record:
>
>    - chr11    128911444    .    T    C
>
> I get ClinVar information for all the transcripts consequences of the
> variant. However If I'm not wrong I should only output ClinVar for those
> consequences with same RefSeq as described by ClinVar, in this case
> "NM_000890.3" associated to RCV000126421.3.
>
> I don't understand exactly how does Ensembl handles Phenotype information
> and if this kind of check is possible. The point should be only output
> phentoypes not only based on variation but check that transcript between
> phentoype and variation is the same.
>
> Regards,
> Guillermo.
>
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