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<p>Thank you Will, that's good to know.</p>
<p><br>
</p>
<p>Cheers,</p>
<p>Alison</p>
<p><br>
</p>
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<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> 05 December 2016 15:50:40<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>Those that remain have no relevant data mapped to them in Ensembl (either transcripts or known variants), so we do not record them in the cache, e.g.</div>
<div><br>
</div>
<div><a href="http://www.ensembl.org/Homo_sapiens/Location/View?r=KI270722.1:1-194050">http://www.ensembl.org/Homo_sapiens/Location/View?r=KI270722.1:1-194050</a><br>
</div>
<div><br>
</div>
<div>VEP shouldn't really warn in these cases, and this will be fixed in a future version.</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 5 December 2016 at 15:38, 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_7280760143326701576divtagdefaultwrapper" style="font-size:12pt;color:#000000;font-family:Calibri,Arial,Helvetica,sans-serif" dir="ltr">
<div id="m_7280760143326701576divtagdefaultwrapper" 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>
<span class="">
<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>
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<div id="m_7280760143326701576divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b>
<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> <<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>> on behalf of Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>><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 class="h5">
<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_7280760143326701576m_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_7280760143326701576m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>160424<span class="m_7280760143326701576m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>.<span class="m_7280760143326701576m_8267717189802556364Apple-tab-span" style="white-space:pre-wrap">
</span>C<span class="m_7280760143326701576m_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="m_7280760143326701576HOEnZb"><font color="#888888">
<div><br>
</div>
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<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>
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The University of Edinburgh is a charitable body, registered in<br>
Scotland, with registration number SC005336.<br>
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