[ensembl-dev] Ensembl REST API | linkage disequilibrium

[Ramiro Magno]

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> wrote:

> 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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