[ensembl-dev] VEP script - per gene and canonical options

[Eva Goncalves Serra]

Hi Will,

This helped a lot, thanks! And great to hear about the change for the next release.

Cheers,

Eva

From: Will McLaren <wm2 at ebi.ac.uk<mailto:wm2 at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Tuesday, 11 February 2014 17:43
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] VEP script - per gene and canonical options

Hello,

There is only one canonical transcript per gene.

--per_gene picks the transcript that gives the most severe consequence type; no account is taken of whether the transcript is canonical. If two or more transcripts give the same consequence, the one chosen is essentially random - if this happens to be the canonical one then it will be shown as such.

This is being tweaked for the next release of VEP (75); priority is given to canonical then protein coding transcripts before consequence rank. There will be a new flag, --pick that picks one consequence per variant according to these criteria. --per_gene will do the same, but will give one per gene if more than one gene is overlapped by the variant.

Hope that helps

Will McLaren
Ensembl Variation


On 11 February 2014 16:31, Eva Goncalves Serra <egs at sanger.ac.uk<mailto:egs at sanger.ac.uk>> wrote:
Hi,

I am using VEP and the option —per_gene to output only the most severe consequence for a gene (the documentation says that the choice of transcript is arbitrary id more than one has the same predicted consequence) and also —canonical to denote whether the transcript is the canonical one or not.
My question is: if using these two options together, is the -canonical option relative to the transcript chosen with the most severe consequence by the –per_gene option?

Thanks a lot,

Eva
--
PhD Student, Wellcome Trust Sanger Institute

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