[ensembl-dev] Ensembl REST API > possible bug in LD endpoints

[Anja Thormann]

Hi Ramiro,

thank you for reporting this. There is indeed a bug in the code which passes the window size parameter to the LD calculation script. The window size used at the moment is set to 200kb instead of the requested 500kb. This will be corrected for our next release which is planned for the second half of September. 

Best regards,
Anja

> On 2 Sep 2019, at 16:39, Ramiro Magno <ramiro.magno at gmail.com> wrote:
> 
> Hi devs,
> 
> When looking for proxy snps of rs7707921, the snp rs17243791 does not show up:
> 
> https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8 <https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8>
> 
> But if I ask for their linkage disequilibrium explicitly:
> 
> https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0 <https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0>
> 
> I can see that they are indeed in LD with an r^2 of 0.920 (above the 0.8 threshold used above).
> 
> The two snps are 215,400 bp away from each other, which is below the 250k up/downstream threshold, i.e. window_size=500.
> 
> Any clue?
> 
> Many thanks in advance, Ramiro Magno
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