[ensembl-dev] Ensembl REST API | linkage disequilibrium

[Anja Thormann]

Hi Ramiro,

the lower bound for d_prime is 0.

Best wishes,
Anja

> On 9 Oct 2019, at 20:03, Ramiro Magno <ramiro.magno at gmail.com> wrote:
> 
> BTW: is there a similar lower bound on d_prime? Or is it 0?
> 
> On Wed, 9 Oct 2019 at 19:36, Ramiro Magno <ramiro.magno at gmail.com <mailto:ramiro.magno at gmail.com>> wrote:
> Hi Anja,
> 
> Thanks!
> 
> Best, RM
> 
> On Wed, 9 Oct 2019 at 18:00, Anja Thormann <anja at ebi.ac.uk <mailto: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 <mailto: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 <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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