<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<style type="text/css" style="display:none;"><!-- P {margin-top:0;margin-bottom:0;} --></style>
</head>
<body dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;" dir="ltr">
<div id="divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif;" dir="ltr">
<p>Hi Will,</p>
<p><br>
</p>
<p>Thanks, have just tested the update. Some of the contig names now work:</p>
<p><br>
</p>
<p></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
</p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr11_KI270721v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr14_GL000009v2</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr14_GL000194v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr14_GL000225v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr14_KI270726v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr15_KI270727v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr16_KI270728v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr17_GL000205v2</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr1_KI270711v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr1_KI270713v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr22_KI270731v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr22_KI270733v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chr22_KI270734v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_GL000195v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_GL000213v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_GL000216v2</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_GL000218v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_GL000219v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_GL000220v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_KI270442v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_KI270744v1</span></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;">chrUn_KI270750v1</span></p>
<br>
<p></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="font-variant-ligatures: no-common-ligatures;"></span></p>
<p>but a large number (131) still give warnings (attached).</p>
<p><br>
</p>
<p>Cheers,</p>
<p>Alison</p>
<p><br>
</p>
<p></p>
<p style="margin: 0px; font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; font-stretch: normal; font-size: 11px; line-height: normal; font-family: Menlo;">
<span style="color: rgb(33, 33, 33); font-family: wf_segoe-ui_normal, "Segoe UI", "Segoe WP", Tahoma, Arial, sans-serif; font-size: 13.3333px;">-- </span><br>
</p>
<div id="Signature">
<div id="divtagdefaultwrapper" style="font-size:12pt; color:#000000; background-color:#FFFFFF; font-family:Calibri,Arial,Helvetica,sans-serif">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Alison Meynert</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">alison.meynert@igmm.ed.ac.uk</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">MRC Human Genetics Unit</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">MRC IGMM</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">University of Edinburgh</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Western General Hospital</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">Crewe Road, Edinburgh EH4 2XU</span><br style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33); font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif; font-size:13.3333330154419px; background-color:rgb(255,255,255)">United Kingdom</span><br>
</div>
</div>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> dev-bounces@ensembl.org <dev-bounces@ensembl.org> on behalf of Will McLaren <wm2@ebi.ac.uk><br>
<b>Sent:</b> 22 November 2016 10:01:25<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] VEP 86 GRCh38 - alt contig names not recognized</font>
<div> </div>
</div>
<div>
<div dir="ltr">Hi Alison,
<div><br>
</div>
<div>Thanks for bringing this to our attention, there was a bug in the way VEP was handling chromosome names beginning with "chr".</div>
<div><br>
</div>
<div>This should be fixed now in the release/86 branch of the ensembl-variation module; if you used INSTALL.pl to set up your command-line VEP then you can re-run this to pick up the changes.</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 21 November 2016 at 15:53, MEYNERT Alison <span dir="ltr">
<<a href="mailto:alison.meynert@igmm.ed.ac.uk" target="_blank">alison.meynert@igmm.ed.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div id="m_8267717189802556364divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif" dir="ltr">
<p>I've been annotating some GRCh38 (hs38DH) VCFs with VEP 86, and it's working fine for the primary assembly, but I'm getting warnings on the alt contig names, e.g.</p>
<p><br>
</p>
<p>WARNING: Chromosome Un_GL000218v1 not found in cache on line 3416412</p>
<div><br>
</div>
<div>It looks like VEP is just chopping the 'chr' prefixes and not fully mapping the alt contig names to the Ensembl-style versions. Both the web interface and the standalone Perl script give the same results; however, interestingly, when I enter a variant
like this into the web interface, e.g. </div>
<div><br>
</div>
<div>
<p style="margin-right:0px;margin-left:0px;font-size:11px;line-height:normal;font-family:Menlo">
<span style="font-variant-ligatures:no-common-ligatures">chrUn_GL000218v1<span class="m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>160424<span class="m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>.<span class="m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>C<span class="m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>CTTT,CTTTT</span></p>
</div>
<div><br>
</div>
<div>And run the "instant VEP", I get a result (see attached screenshot). If I fix the contig name manually to GL000218.1, I get full results.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Alison</div>
<span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div id="m_8267717189802556364Signature">
<div id="m_8267717189802556364divtagdefaultwrapper" style="font-size:12pt;color:#000000;background-color:#ffffff;font-family:Calibri,Arial,Helvetica,sans-serif">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">-- </span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">Alison Meynert</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)"><a href="mailto:alison.meynert@igmm.ed.ac.uk" target="_blank">alison.meynert@igmm.ed.ac.uk</a></span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">MRC Human Genetics Unit</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">MRC IGMM</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">University of Edinburgh</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">Western General Hospital</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">Crewe Road, Edinburgh EH4 2XU</span><br style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">
<span style="color:rgb(33,33,33);font-family:wf_segoe-ui_normal,'Segoe UI','Segoe WP',Tahoma,Arial,sans-serif;font-size:13.3333330154419px;background-color:rgb(255,255,255)">United Kingdom</span><br>
</div>
</div>
</font></span></div>
</div>
<br>
The University of Edinburgh is a charitable body, registered in<br>
Scotland, with registration number SC005336.<br>
<br>
______________________________<wbr>_________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" rel="noreferrer" target="_blank">
http://lists.ensembl.org/<wbr>mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer" target="_blank">
http://www.ensembl.info/</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</body>
</html>