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

[Guillermo Marco Puche]

Hello Will,

Thank you for the information.

Best regards,
Guillermo.

On 11/05/2013 03:39 PM, Will McLaren wrote:
> 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 
> <mailto: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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