<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 Nicolas,<div class=""><br class=""></div><div class="">Thanks for your enquiry. This is expected behaviour, these flags return the somatic status, whether the existing variant is associated with a phenotype, or whether the overlapping gene is associated with a phenotype. The symbol & is used to separate values if multiple existing variants are found to overlap with the input data.</div><div class=""><br class=""></div><div class="">More information on these outputs can be found here: <a href="https://www.ensembl.org/info/docs/tools/vep/vep_formats.html" class="">https://www.ensembl.org/info/docs/tools/vep/vep_formats.html</a></div><div class=""><br class=""></div><div class="">If there’s anything else I can do to help, please let me know.</div><div class=""><br class=""></div><div class="">Kind Regards,</div><div class="">Andrew Parton <br class=""><div><br class=""><blockquote type="cite" class=""><div class="">On 26 Mar 2018, at 17:10, Nicolas Thierry-Mieg <<a href="mailto:Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr" class="">Nicolas.Thierry-Mieg@univ-grenoble-alpes.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">Dear colleagues,<br class=""><br class="">I am running VEP latest (release/91), in offline mode with --gene_phenotype --check_existing .<br class=""><br class="">All I get in the SOMATIC, PHENO and GENE_PHENO columns are strings that look like boolean flags: "0&1" , "1", "0&1&1" ...<br class=""><br class="">I tried against both the default ENSEMBL cache and the refseq cache, with the same results.<br class=""><br class="">Full command-line:<br class="">vep --offline --vcf --no_stats --gene_phenotype --check_existing -i test.vcf -o test_vep.vcf<br class=""><br class="">Is this expected behavior, and if yes how do I interpret these values?<br class="">Otherwise, any suggestions? Re-install VEP from scratch? Clear and re-install the cache? Something else?<br class=""><br class="">Thanks.<br class="">Regards,<br class="">Nicolas<br class="">_______________________________________________<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></div></blockquote></div><br class=""></div></body></html>