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

[Guillermo Marco Puche]

Hello Will,

Thank you for your quick response. That was my guess.

Regards,
Guillermo.

On 20/06/16 15:28, Will McLaren wrote:
> 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 
> <mailto: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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