[ensembl-dev] 'Canonical' splice site change with VEP

Will McLaren wm2 at ebi.ac.uk
Mon Apr 18 14:47:28 BST 2016


Hi Adam,

The SO term splice_donor_variant [1] as reported by the VEP covers this.
Variants in the receiving 2bp region are defined as splice_acceptor_variant
[2].

There's also a number of splicing predictors available as VEP plugins (e.g.
[3]) which you may find useful.

Regards

Will McLaren
Ensembl Variation

[1] : http://www.sequenceontology.org/miso/current_svn/term/SO:0001575
[2] : http://www.sequenceontology.org/miso/current_svn/term/SO:0001574
[3] : https://github.com/Ensembl/VEP_plugins/blob/release/84/GeneSplicer.pm

On 18 April 2016 at 11:14, Levine, Adam <a.levine at ucl.ac.uk> wrote:

> Is there a way of getting VEP to identify whether a variant causes a
> 'canonical' splice site change (i.e. affects the first two nucleotides
> flanking an exon)?
>
> Thank you,
>
> Adam
>
> Adam P. Levine
>
> _______________________________________________
> 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/20160418/39bbd461/attachment.html>


More information about the Dev mailing list