<div dir="ltr">BTW: is there a similar lower bound on d_prime? Or is it 0?<br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 9 Oct 2019 at 19:36, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com">ramiro.magno@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Hi Anja,<br><div><br></div><div>Thanks!</div><div><br></div><div>Best, RM</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Wed, 9 Oct 2019 at 18:00, Anja Thormann <<a href="mailto:anja@ebi.ac.uk" target="_blank">anja@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div>Hi Ramiro,<div><br></div><div>our <a href="https://github.com/Ensembl/ensembl-variation/blob/release/98/C_code/ld_vcf.c#L44" target="_blank">script</a> 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.</div><div><br></div><div>Best wishes,</div><div>Anja<br><div><br><blockquote type="cite"><div>On 9 Oct 2019, at 17:42, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com" target="_blank">ramiro.magno@gmail.com</a>> wrote:</div><br><div><div dir="ltr">Hi Devs,<br><div><br></div><div>I was expecting to retrieve the LD between these two variants rs7707921 and rs10036319:</div><div><br></div><div><a href="https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs10036319?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0" target="_blank">https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs10036319?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0</a><br></div><div><br></div><div>But nothing is returned. These variants are both on chromosome 5 and within the threshold distance.</div><div><br></div><div>Many thanks!</div><div><br></div><div>RM</div></div>
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