[ensembl-dev] Ensembl REST API | linkage disequilibrium

[Ramiro Magno]

Hi Anja,

Thanks!

Best, RM

On Wed, 9 Oct 2019 at 18:00, Anja Thormann <anja at ebi.ac.uk> wrote:

> Hi Ramiro,
>
> our script
> <https://github.com/Ensembl/ensembl-variation/blob/release/98/C_code/ld_vcf.c#L44> for
> calculating LD filters out results with r2 values that are smaller than
> 0.05. I will need to update the documentation for choosing a threshold for
> the r2 value to reflect that.
>
> Best wishes,
> Anja
>
> On 9 Oct 2019, at 17:42, Ramiro Magno <ramiro.magno at gmail.com> wrote:
>
> Hi Devs,
>
> I was expecting to retrieve the LD between these two variants rs7707921
> and rs10036319:
>
>
> https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs10036319?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0
>
> But nothing is returned. These variants are both on chromosome 5 and
> within the threshold distance.
>
> Many thanks!
>
> RM
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