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

[Will McLaren]

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> 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
>
>
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