<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="">Dear Julie,<div class=""><div class=""><br class=""></div><div class="">the GERP score on the variant summary page is retrieved from the BigWig file: <a href="ftp://ftp.ensembl.org/pub/current_compara/conservation_scores/103_mammals.gerp_conservation_score/gerp_conservation_scores.homo_sapiens.GRCh38.bw" class="">ftp://ftp.ensembl.org/pub/current_compara/conservation_scores/103_mammals.gerp_conservation_score/gerp_conservation_scores.homo_sapiens.GRCh38.bw</a>. We are using a parser which has been written for project internal purposes and is not as well documented for use outside of the project. However, I would be happy to send you a small perl script which makes use of Ensembl's APIs to retrieve GERP scores by location from the BigWig file. Alternatively, you can also use a BigWig parser of your choice.</div><div class=""><br class=""></div><div class="">You can also use this <a href="https://github.com/Ensembl/ensembl-compara/blob/release/100/scripts/examples/dna_getConservationScores.pl" class="">script</a> which is provided by Ensembl's compara API for retrieving GERP scores. You just need to modify the region parameters at the top of the script. </div><div class=""><br class=""></div><div class="">The EMF file format is explained in more detail here: <a href="ftp://ftp.ensembl.org/pub/release-100/emf/ensembl-compara/multiple_alignments/103_mammals.epo_low_coverage/README.emf" class="">ftp://ftp.ensembl.org/pub/release-100/emf/ensembl-compara/multiple_alignments/103_mammals.epo_low_coverage/README.emf</a></div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Anja</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On 6 Jul 2020, at 15:09, Julie Sullivan <<a href="mailto:julie.sullivan@gmail.com" class="">julie.sullivan@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><a href="http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=1:31789941-31789941;v=rs1286699429;vdb=variation;vf=502464213" class="">http://www.ensembl.org/Homo_sapiens/Variation/Explore?db=core;r=1:31789941-31789941;v=rs1286699429;vdb=variation;vf=502464213</a><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">On that page is a gerp score <span class="gmail-text_separator"></span><span class=""><span class="gmail-_ht gmail-ht"><span class="gmail-_ht gmail-ht">GERP</span></span>: 1.27. Where can I download that GERP score?</span><br class=""><br class="">I found this: <a href="https://www.ensembl.org/Help/Faq?id=221" class="">https://www.ensembl.org/Help/Faq?id=221</a><br class=""><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Which says to get the gerp scores from an EMF file. I am unfamiliar with this file type. (apparently emf is also a image file type, so google didn't help!)<br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><a href="ftp://ftp.ensembl.org/pub/current_emf/ensembl-compara/multiple_alignments/103_mammals.epo_low_coverage/103_mammals.epo_low_coverage.1_10.emf.gz" class="">ftp://ftp.ensembl.org/pub/current_emf/ensembl-compara/multiple_alignments/103_mammals.epo_low_coverage/103_mammals.epo_low_coverage.1_10.emf.gz</a></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">The EMF file looks like this:<br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br class="">##FORMAT (compara)<br class="">##DATE Fri Feb 21 15:26:12 2020<br class="">##RELEASE 100<br class=""># Alignments: 103 eutherian mammals EPO-Low-Coverage<br class=""># Region: Homo sapiens chromosome:GRCh38:10:1:133797422:1<br class=""># File 1<br class=""><br class="">SCORE 103 eutherian mammals GERP Conservation Scores<br class="">ID 18230001887772<br class="">DATA<br class="">aAAaaaaaaAaAAGGGGA-AAA---A--AAA-AA---CC-A -1.03 <-- which position is this score for? <br class="">cCCccccccCcCCCCCCC-CCC---T--CCC-TC---TT-C -1.97<br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">1. is this file the right place to get the GERP scores listed on the website?<br class="">2. Does each line represent a position? So "-1.03" would be the score for position chr10:1? Or is there a way to find out which positions are being described? Or am I reading this file wrong? Because position 1 doesn't make a lot of sense but I don't see another number.<br class=""><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Thank you!<br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">Julie<br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><br class="">=====<br class=""><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small">I also tried the Perl API and this file but was not successful:<span class=""></span><br class=""></div><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><span class=""></span><div class="gmail_default" style="font-family:trebuchet ms,sans-serif;font-size:small"><span class=""><br class=""><a href="ftp://ftp.ensembl.org/pub/current_compara/conservation_scores/103_mammals.gerp_conservation_score/" class="">ftp://ftp.ensembl.org/pub/current_compara/conservation_scores/103_mammals.gerp_conservation_score/</a><a class="gmail-file" href="ftp://ftp.ensembl.org/pub/current_compara/conservation_scores/103_mammals.gerp_conservation_score/gerp_conservation_scores.homo_sapiens.GRCh38.bw">gerp_conservation_scores.homo_sapiens.GRCh38.bw</a></span></div></div></div>
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