<html><head><meta http-equiv="Content-Type" content="text/html; charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class=""><div class="">Hi Ramiro,</div><div class=""><br class=""></div>the lower bound for d_prime is 0.<div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Anja<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 9 Oct 2019, at 20:03, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com" class="">ramiro.magno@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">BTW: is there a similar lower bound on d_prime? Or is it 0?<br class=""></div><br class=""><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" class="">ramiro.magno@gmail.com</a>> wrote:<br class=""></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" class="">Hi Anja,<br class=""><div class=""><br class=""></div><div class="">Thanks!</div><div class=""><br class=""></div><div class="">Best, RM</div></div><br class=""><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" class="">anja@ebi.ac.uk</a>> wrote:<br class=""></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div class="">Hi Ramiro,<div class=""><br class=""></div><div class="">our <a href="https://github.com/Ensembl/ensembl-variation/blob/release/98/C_code/ld_vcf.c#L44" target="_blank" class="">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 class=""><br class=""></div><div class="">Best wishes,</div><div class="">Anja<br class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 9 Oct 2019, at 17:42, Ramiro Magno <<a href="mailto:ramiro.magno@gmail.com" target="_blank" class="">ramiro.magno@gmail.com</a>> wrote:</div><br class=""><div class=""><div dir="ltr" class="">Hi Devs,<br class=""><div class=""><br class=""></div><div class="">I was expecting to retrieve the LD between these two variants rs7707921 and rs10036319:</div><div class=""><br class=""></div><div class=""><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" class="">https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs10036319?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0</a><br class=""></div><div class=""><br class=""></div><div class="">But nothing is returned. These variants are both on chromosome 5 and within the threshold distance.</div><div class=""><br class=""></div><div class="">Many thanks!</div><div class=""><br class=""></div><div class="">RM</div></div>
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