[ensembl-dev] Wild-type variation allele from 1000 genomes

[Will McLaren]

Hi Guillermo,

I assume by "wild-type" you mean the most common or major allele?

The minor allele is listed by the VEP when you use --gmaf, as well as in
our Ensembl MySQL databases, along with the allele string (the list of all
alleles) so it should be fairly trivial to work out which is the major or
wild-type allele from that information.

You will see rare cases where there are more than two alleles in the allele
string; in this case you could assume that the first allele in the allele
string is the one you want (since we put the reference allele first in this
string where we can).

You could do this in a plugin for the VEP, or extract the data from the
MySQL table and run a quick script over it.

In a plugin you'd need to access the $tva->variation_feature->{existing}
data structure to see the fields you require.

Regards

Will McLaren
Ensembl Variation


On 5 November 2013 14:18, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Dear devs,
>
> I know at this moment VEP script offers population frecuencies from 1000
> genomes project, which is awesome.
>
> I would like to know if it's possible to retrieve the "wild-type allele"
> from 1000 genomes project for each variation position. As you may know
> variation allele may be biased due to the human reference we use (it's very
> uncommon but it does happen).
>
> I don't know if this information is included in ensembl database or is
> going to be introduceded in near future.
>
>
> Thank you.
>
> Best regards,
> Guillermo.
>
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