[ensembl-dev] SNP - Gene filtering queries

[Laurent Gil]

Dear Manos,

One alternative solution would be to use the Ensembl REST API - Overlap 
endpoint <https://rest.ensembl.org/documentation/info/overlap_id> (1 
gene at a time).
e.g.: 
https://rest.ensembl.org/overlap/id/ENSG00000182533?content-type=application/json;feature=variation

However this might take some times for the genes overlapping a great 
number of variants.

Otherwise, you could use directly the Ensembl Perl API.

I hope this helps.

Best regards,

Laurent

On 08/10/2018 09:47, ea8 wrote:
>
> Hi,
>
>
> I am using biomaRt to query the ensembl for SNPs using 50-300 genes as 
> filter option.
>
> However this process is very time consuming and most of the times i am 
> getting errors.
>
> I also used the command in for loop by querying one gene at the time 
> and then combine the list.
>
> I would like to ask if there is a faster way to query the SNPs. The 
> only information i need is the SNP id and the Gene id.
>
> Best,
>
> Manos
>
>
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