<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">Hi Danny,<div class=""><br class=""></div><div class=""><div class="">you will get the most detailed information on the merge history of an rs id from dbSNP.</div><div class=""><br class=""></div><div class="">I recommend that you take a look at dbSNP's API:</div><div class=""><a href="https://api.ncbi.nlm.nih.gov/variation/v0/" class="">https://api.ncbi.nlm.nih.gov/variation/v0/</a></div><div class=""><br class=""></div><div class="">Or flat files from:</div><div class=""><a href="https://ftp.ncbi.nih.gov/snp/latest_release/" class="">https://ftp.ncbi.nih.gov/snp/latest_release/</a></div><div class="">This file contains the merge information: <a href="https://ftp.ncbi.nih.gov/snp/latest_release/JSON/refsnp-merged.json.bz2" class="">https://ftp.ncbi.nih.gov/snp/latest_release/JSON/refsnp-merged.json.bz2</a></div><div class=""><br class=""></div><div class="">And here is an example of using the API:</div><div class="">Getting information for rs10001600 (<a href="https://www.ncbi.nlm.nih.gov/snp/rs10001600" class="">https://www.ncbi.nlm.nih.gov/snp/rs10001600</a>):</div><div class=""><a href="https://api.ncbi.nlm.nih.gov/variation/v0/beta/refsnp/10001600" class="">https://api.ncbi.nlm.nih.gov/variation/v0/beta/refsnp/10001600</a> where merged_snapshot_data stores the id history.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class="">We are not extracting the full merge history for each rs id into Ensembl and therefore wouldn’t give a complete picture and decided against adding this information into our data dumps.</div><div class=""><br class=""></div><div class="">Best wishes,</div><div class="">Anja</div><div class=""><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On 18 Feb 2021, at 18:08, Andrew Parton <<a href="mailto:aparton@ebi.ac.uk" class="">aparton@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; line-break: after-white-space;" class="">Hi Danny,<div class=""><br class=""></div><div class="">Currently, we do not have a file contains all of these mappings. However, VEP will allow you to annotate your VCFs with the variation synonym data that we have, by providing known synonyms for colocated variants: <a href="https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_var_synonyms" class="">https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_var_synonyms</a></div><div class=""><br class=""></div><div class="">Additionally, it may be possible for us to generate these synonyms in a single file as part of our next release, however VEP should be a quicker solution for you.</div><div class=""><br class=""></div><div class="">Kind Regards,</div><div class="">Andrew</div><div class=""> </div><div class=""><div class=""><br class=""><blockquote type="cite" class=""><div class="">On 12 Feb 2021, at 05:29, <a href="mailto:danny.kunz@gmx.de" class="">danny.kunz@gmx.de</a> wrote:</div><br class="Apple-interchange-newline"><div class=""><meta charset="UTF-8" class=""><div class="WordSection1" style="page: WordSection1; caret-color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; text-decoration: none;"><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Hi all,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Quick question:<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Our pipeline has to deal with VCF from older assembly releases from the GRCH37 branch.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">We tried utilizing the FTP variation VCF files, but realized that we only have hits in about 40% of the patient VCF ids matched within the FTP variation data.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Obviously the old rs ids (synonyms) from the older assemblies are not contained in those newer releases.<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Is there any file on the FTP which contains those synonym mappings?<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">-<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Calling the REST api does not cause a problem with the old rs ids as it translates them to the newer ones, but if we want to reduce the REST communication overhead, it would be helpful to be able to achieve the same with the FTP data, right?<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class=""><o:p class=""> </o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Thanks,<o:p class=""></o:p></div><div style="margin: 0cm; font-size: 11pt; font-family: Calibri, sans-serif;" class="">Danny<o:p class=""></o:p></div></div><span style="caret-color: rgb(0, 0, 0); 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