[ensembl-dev] VEP input file format question

[Will McLaren]

Hi Dylan,

The strand of the alleles you give is specified in the 5th column; in the
example you cite, the strand is "-", so the reverse/negative strand.

This means the CGT is the reference sequence on the reverse strand; it
would therefore be ACG (since the sequence is reversed as well as
complemented) on the forward strand for the same given coordinates.

Regards

Will McLaren
Ensembl Variation


On 17 March 2014 09:40, Dylan Spalding <spalding at ebi.ac.uk> wrote:

> Hi,
>
> I just want to confirm which strand the reference allele is given as in
> the default VEP input fomat.
>
> For example,
>
> 8   12600     12602     CGT/- -
>
> as given here: http://www.ensembl.org/info/docs/tools/vep/vep_formats.html,
>
> does CGT refer to the allele on the + strand or the deleted allele on the
> - strand?
>
> Thanks,
>
> Dylan.
>
> --
> Dylan Spalding
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> United Kingdom
> Email spalding at ebi.ac.uk
>
>
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