<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Anja,</div><div class=""><br class=""></div><div class="">Thanks for the quick response.</div><div class=""><br class=""></div><div class="">Yes, pulling a fresh ensembl-variation seems to have solved it .. smile.</div><div class=""><br class=""></div><div class="">Thanks also for confirming the handling of non-biallelics.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">Andrew</div><br class=""><div><blockquote type="cite" class=""><div class="">On Jul 18, 2016, at 11:55 AM, Anja Thormann <<a href="mailto:anja@ebi.ac.uk" class="">anja@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Hi Andrew,</div><div class=""><br class=""></div><div class="">I think we fixed the bug you are describing in 2). Could you please pull the changes from ensembl-variation/release-84 branch and check if that is solving the problem?</div><div class=""><br class=""></div><div class="">For 1) yes, we are calculating LD only for bi-allelic variants at the moment. It would definitely be great to extend the computation to multi-allelic variants. We will keep you updated about any progress we are going to do with this.</div><div class=""><br class=""></div><div class="">Regards,</div><div class="">Anja</div><div class=""><br class=""></div><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 17 Jul 2016, at 11:19, <a href="mailto:andrew126@mac.com" class="">andrew126@mac.com</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta http-equiv="Content-Type" content="text/html charset=us-ascii" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi,<div class=""><br class=""></div><div class="">I am using API 84 on Ubuntu (64-bit).</div><div class=""><br class=""></div><div class="">1)</div><div class=""><br class=""></div><div class="">Is it correct that LD will not be calculated for any variants having more than 2 alleles? (It looks like being biallelic is a very hard coded requirement of calc_genotypes.c)</div><div class=""><br class=""></div><div class="">2)</div><div class=""><br class=""></div><div class="">I am confused by some discrepancies I see with the Ensembl LD calculations vrs. other LD calculators.</div><div class=""><br class=""></div><div class="">As an example, imagine I want all variants in high LD with rs13181561 that occur in a particular slice.</div><div class=""><br class=""></div><div class="">LD calculations using the below perl API script find an r^2 of >0.6 between rs13181561 and rs372693892.</div><div class=""><br class=""></div><div class="">This is confusing because no other LD calculators find this result, and Ensembl's web page on the variant indicates that no sample genotypes are available:</div><div class=""><br class=""></div><div class=""><a href="http://useast.ensembl.org/Homo_sapiens/Variation/Explore?r=5:139447545-139448545;v=rs372693892;vdb=variation;vf=54723062" class="">http://useast.ensembl.org/Homo_sapiens/Variation/Explore?r=5:139447545-139448545;v=rs372693892;vdb=variation;vf=54723062</a></div><div class=""><br class=""></div><div class="">Further, the script does NOT find rs7446197 as being in high LD with rs13181561 (other engines find it to have r^2 > 0.6).</div><div class=""><br class=""></div><div class="">I do not know if there is any complication because both rs372693892 and rs7446197 have the same genomic location?</div><div class=""><br class=""></div><div class="">Can you provide some guidance on this?</div><div class=""><br class=""></div><div class="">Please let me know if any other information would be useful.</div><div class=""><br class=""></div><div class="">Thanks very much.</div><div class=""><br class=""></div><div class="">Best,</div><div class=""><br class=""></div><div class="">Andrew</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><div class="">use strict;</div><div class="">$|=1;</div><div class="">use IPC::Run;</div><div class="">use Bio::EnsEMBL::Registry;</div><div class=""><br class=""></div><div class="">use Bio::EnsEMBL::ApiVersion; </div><div class="">printf( "The API version used is %s\n", software_version() ); </div><div class=""><br class=""></div><div class="">my $registry = 'Bio::EnsEMBL::Registry';</div><div class="">$registry->load_all();</div><div class="">$registry->set_reconnect_when_lost(1);</div><div class="">$registry->load_registry_from_db(</div><div class=""> -host => '<a href="http://useastdb.ensembl.org/" class="">useastdb.ensembl.org</a>',</div><div class=""> -user => 'anonymous'</div><div class=""> );</div><div class=""><br class=""></div><div class=""><div class="">my $slice_adaptor = $registry->get_adaptor('human', 'core', 'slice');</div><div class="">my $population_adaptor = $registry->get_adaptor('human', 'variation', 'population');</div><div class="">my $ldFeatureContainerAdaptor = $registry->get_adaptor('human', 'variation', 'ldfeaturecontainer');</div><div class="">$ldFeatureContainerAdaptor->db->use_vcf(1);</div><div class="">$registry->set_reconnect_when_lost(1);</div></div><div class=""><br class=""></div><div class="">my $pop = "1000GENOMES:phase_3:AMR";</div><div class="">my $chr = 5;</div><div class="">my $low = 139445000;</div><div class="">my $high = 139475000;</div><div class=""><br class=""></div><div class="">my $slice = $slice_adaptor->fetch_by_region('chromosome',$chr,$low,$high); </div><div class="">my $population = $population_adaptor->fetch_by_name($pop);</div><div class="">my $ldFeatureContainer = $ldFeatureContainerAdaptor->fetch_by_Slice($slice,$population);</div><div class="">foreach my $r_square (@{$ldFeatureContainer->get_all_r_square_values}){</div><div class=""> if ($r_square->{r2} >= 0.05){ </div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>if ($r_square->{variation1}->variation_name eq "rs13181561" || $r_square->{variation2}->variation_name eq "rs13181561") {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span> print "High r2 (".($r_square->{r2}).") between variations ", $r_square->{variation1}->variation_name, "-", $r_square->{variation2}->variation_name, " in $pop\n";</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>}</div><div class=""> }</div><div class="">}</div><div class=""><br class=""></div></div><div class="">Output from script:</div><div class=""><br class=""></div><div class=""><div class="">High r2 (0.692506) between variations rs11954057-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.625299) between variations rs372693892-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.900663) between variations rs111805170-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.686462) between variations rs10463977-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.264367) between variations rs28419191-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.375759) between variations rs7380062-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.903044) between variations rs13181561-rs13153461 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.898459) between variations rs71574449-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.883522) between variations rs13181561-rs55792153 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.360986) between variations rs73257323-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.898459) between variations rs9716069-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.702607) between variations rs763007006-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.533529) between variations rs34149439-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.096040) between variations rs114079768-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.286249) between variations rs10875554-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.853556) between variations rs34580585-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.702607) between variations rs36137978-rs13181561 in 1000GENOMES:phase_3:AMR</div><div class="">High r2 (0.088433) between variations rs140049780-rs13181561 in 1000GENOMES:phase_3:AMR</div></div></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></div>_______________________________________________<br class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a><br class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a><br class=""></div></blockquote></div><br class=""></body></html>