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

[Levine, Adam]

Thank you very much Will.

Kind regards,

Adam

Adam P. Levine

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 18 April 2016 14:47
To: Ensembl developers list
Subject: Re: [ensembl-dev] 'Canonical' splice site change with VEP

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<mailto: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

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