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

[Ramiro Magno]

Hi Anja,

Thanks for clarifying this!

Cheers, RM


On Thu, 18 Jul 2019 at 10:20, Anja Thormann <anja at ebi.ac.uk> wrote:

> 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,
> Anja
>
>
> 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
>
> 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
>
> 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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