<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">
<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="Apple-tab-span" style="white-space:pre">
</span>160424<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre">
</span>C<span class="Apple-tab-span" style="white-space:pre"> </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>
<div><br>
</div>
<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)">-- </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)">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>
</body>
</html>