[ensembl-dev] LD through Biomart

[Will McLaren]

Hi G,

This is not possible due to the size of the data.

The LD data you see on the Ensembl website is calculated on the fly from
the genotype data stored in the database. If you imagine a sliding 20kb
window (the default size), where in each window you have to store the LD
values between each possible pair of SNPs, you can see that this data gets
very large very quickly. This volume of data is not suited to the way that
BioMart works.

We have considered in the past creating dumps of this data to present on
the FTP site; we can look at this again if there is interest.

Regards

Will McLaren
Ensembl Variation

On 8 December 2014 at 16:38, Genomeo Dev <genomeodev at gmail.com> wrote:

> Hi,
>
> Anyone knows if is possible to retrieve LD values for a region arround a
> variant in Ensembl Biomart?
>
> Thanks.
> --
> G.
>
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