[ensembl-dev] Ensembl REST API | Bug in ld/:species/pairwise/:id1/:id2?

Anja Thormann anja at ebi.ac.uk
Thu Jul 18 10:20:18 BST 2019

Hi Ramiro,

this is not a bug as such because we did not intend to keep the order of the input variants which we loose in our internal LD calculations. But I absolutely agree that this is causing confusions and we will update the endpoint to retain the order of the input variants in the output. This will be updated for our 98 release planned to be out in September.

Best wishes,

> On 17 Jul 2019, at 17:41, Ramiro Magno <ramiro.magno at gmail.com> wrote:
> Hi
> It seems that the response returned by this endpoint:
> http://rest.ensembl.org/documentation/info/ld_pairwise_get <http://rest.ensembl.org/documentation/info/ld_pairwise_get>
> does not always respect what is variant id1 and variant id2.
> Example:
> https://rest.ensembl.org/ld/human/pairwise/rs1042779/rs62255400?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0 <https://rest.ensembl.org/ld/human/pairwise/rs1042779/rs62255400?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0>
> As per the documentation, I was expecting variant1 = rs1042779, and variant2 = rs62255400 but the actual response is:
>   d_prime: '0.999977'
>   population_name: 1000GENOMES:phase_3:CEU
>   r2: '0.271200'
>   variation1: rs62255400
>   variation2: rs1042779
> The two variants are swapped.
> Can you confirm this is a bug?
> Cheers, Ramiro
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