[ensembl-dev] LD through Biomart

[Genomeo Dev]

Thanks Will. Yes if you could provide FTP dumps of that it would be very
useful.

G.

On 9 December 2014 at 16:23, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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>
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>


-- 
G.
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