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

[Ramiro Magno]

🤓👍

On Tue, 3 Sep 2019 at 09:51, Anja Thormann <anja at ebi.ac.uk> wrote:

> 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
>
> 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
>
> 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
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20190903/218cd797/attachment.html>