[ensembl-dev] How does the web VEP HGVS annotator choose RefSeq transcripts?

[Luke Goodsell]

Hi Will,

That’s very helpful, thank you.

Kind regards,
Luke

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
Sent: 28 July 2016 09:21
To: Ensembl developers list
Subject: Re: [ensembl-dev] How does the web VEP HGVS annotator choose RefSeq transcripts?

Hi Luke,

When the VEP uses RefSeq transcripts it is in fact using the reference genome sequence to generate its predictions. RefSeq transcript models are mapped to the reference genome and the sequence retrieved from those mapped coordinates is used. This means that if a RefSeq differs from the genome, you may see unexpected results WRT to the RefSeq sequence. [1]

Each mapped transcript is analysed independently, though you may have VEP choose only one to analyse using any of the --pick flags [2].

Hope that helps

Will McLaren
Ensembl Variation

[1] : http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#refseq
[2] : http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick

On 27 July 2016 at 21:42, Luke Goodsell <Luke.Goodsell at ogt.com<mailto:Luke.Goodsell at ogt.com>> wrote:
Hi,

Could you please let me know by what criteria the VEP HGVS annotator chooses RefSeq transcripts as a reference? Ie, how does it choose which of the intersecting transcripts to use as the reference?

Kind regards,
Luke


Disclaimer

The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful.

This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more Click Here<http://www.mimecast.com/products/>.

_______________________________________________
Dev mailing list    Dev at ensembl.org<mailto:Dev at ensembl.org>
Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
Ensembl Blog: http://www.ensembl.info/

Disclaimer

The information contained in this communication from the sender is confidential. It is intended solely for use by the recipient and others authorized to receive it. If you are not the recipient, you are hereby notified that any disclosure, copying, distribution or taking action in relation of the contents of this information is strictly prohibited and may be unlawful.

This email has been scanned for viruses and malware, and may have been automatically archived by Mimecast Ltd, an innovator in Software as a Service (SaaS) for business. Providing a safer and more useful place for your human generated data. Specializing in; Security, archiving and compliance. To find out more visit the Mimecast website.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160729/a1bf02d6/attachment.html>