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

[Will McLaren]

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> 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
>
> _______________________________________________
> 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/20140211/3e2cb670/attachment.html>