<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="">Hi Ramiro,<div class=""><br class=""></div><div class="">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. </div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Anja<br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 2 Sep 2019, at 16:39, 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="">Hi devs,<div class=""><br class=""></div><div class="">When looking for proxy snps of rs7707921, the snp rs17243791 does not show up:</div><div class=""><br class=""></div><div class=""><a href="https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8" class="">https://rest.ensembl.org/ld/homo_sapiens/rs7707921/1000GENOMES:phase_3:CEU?window_size=500;d_prime=0;r2=0.8</a><br class=""></div><div class=""><br class=""></div><div class="">But if I ask for their linkage disequilibrium explicitly:</div><div class=""><br class=""></div><div class=""><a href="https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0" class="">https://rest.ensembl.org/ld/homo_sapiens/pairwise/rs7707921/rs17243791?population_name=1000GENOMES:phase_3:CEU;d_prime=0;r2=0</a><br class=""></div><div class=""><br class=""></div><div class="">I can see that they are indeed in LD with an r^2 of 0.920 (above the 0.8 threshold used above).</div><div class=""><br class=""></div><div class="">The two snps are 215,400 bp away from each other, which is below the 250k up/downstream threshold, i.e. window_size=500.</div><div class=""><br class=""></div><div class="">Any clue?</div><div class=""><br class=""></div><div class="">Many thanks in advance, Ramiro Magno</div></div>
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