<div dir="ltr">Hi Guillermo,<div><br></div><div>Are you also running your own database server?</div><div><br></div><div>The GRCh37 v76 databases are hosted on a different port on <a href="http://ensembldb.ensembl.org">ensembldb.ensembl.org</a> (3337); to get the VEP to use this you can add the flag --port 3337 to your command line. If you don't use the DB (most VEP functionality does not use the DB at all, see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations">http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#limitations</a>), you can bypass this completely and use --offline. See <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly">http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#assembly</a> for more details.</div><div><br></div><div>If you are using your own DB server then you will need to make sure you have mirrored the correct human databases; you should have homo_sapiens_*_76_37 (* being core, variation and funcgen).</div><div><br></div><div>HTH</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 15 September 2014 09:04, Guillermo Marco Puche <span dir="ltr"><<a href="mailto:guillermo.marco@sistemasgenomicos.com" target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066">
I forgot to mention than I've already tried to specify assembly with
VEP "--assembly" flag:<br>
<br>
ERROR: Assembly version specified by --assembly (GRCh37) and
assembly.default meta key (GRCh38) do not match<br>
<br>
<div>El 15/09/14 a las #4, Guillermo Marco
Puche escribió:<br>
</div>
<blockquote type="cite"><div><div class="h5">
Hello,<br>
<br>
I installed Ensembl 76 on my local server. I'm not ready yet to
annotate variants vs GRCh38.<br>
I thought that ensembl 76 version supports both GRCh37 and GRCh38.
I downloaded 76 vep cache for GRCh37:<br>
<br>
<a href="ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz" target="_blank">ftp://ftp.ensembl.org/pub/release-76/variation/VEP/homo_sapiens_merged_vep_76_GRCh37.tar.gz</a><br>
<br>
I get the following error:<br>
<br>
<b>ERROR: Cache assembly version (GRCh37) and database or selected
assembly version (GRCh38) do not match.</b><b><br>
</b><br>
I got a bit confused since I saw both cache for GRCh37/38, I would
like to know if in Ensembl 76 I can stilll annotate with GRCh37 or
I just have to move asap to GRCh38 to use 76 version.<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
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<p><span style="font-size:12px"><span style="font-family:arial,helvetica,sans-serif"><span style="color:#000066"><strong>Guillermo Marco
Puche</strong><br>
<br>
Bioinformatician, Computer Science Engineer<br>
Sistemas Genómicos S.L.<br>
Phone: <a href="tel:%2B34%20902%20364%20669" value="+34902364669" target="_blank">+34 902 364 669</a> (Ext.777)<br>
Fax: <a href="tel:%2B34%20902%20364%20670" value="+34902364670" target="_blank">+34 902 364 670</a></span><br>
<a href="http://www.sistemasgenomicos.com" target="_blank"><span style="color:#000066">www.sistemasgenomicos.com</span></a></span></span></p>
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