<div dir="ltr">Hello<div><br></div><div>Shifting HGVS became the default in release 80. You may disable it with "--shift_hgvs 0".<div><br></div><div>In release 79 (and 77, 78 and 79), you had to enable it with "--shift_hgvs".</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div></div><div class="gmail_extra"><br><div class="gmail_quote">On 8 July 2015 at 15:51, Ullman-Cullere, Mollie <span dir="ltr"><<a href="mailto:MULLMANCULLERE@partners.org" target="_blank">MULLMANCULLERE@partners.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div lang="EN-US" link="blue" vlink="purple">
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Question:<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">If --shift_hgvs works in VEPv79, is it on by default, as it is with VEPv80?
<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">We’re running v79 without this flag and want to confirm that we’ll not see the shift.<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Thanks in advance,<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d">Mollie<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal" style="margin-bottom:12.0pt"><i><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Mollie Ullman-Cullere<br>
Sr. Clinical Bioinformaticist<br>
Clinical and Translational Informatics<br>
Dana-Farber Cancer Institute/Partners Healthcare<br>
Cell: <a href="tel:617-817-1496" value="+16178171496" target="_blank">617-817-1496</a></span></i><i><span style="font-size:10.0pt;font-family:"Verdana","sans-serif";color:black"><u></u><u></u></span></i></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1f497d"><u></u> <u></u></span></p>
<div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> <a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a> [mailto:<a href="mailto:dev-bounces@ensembl.org" target="_blank">dev-bounces@ensembl.org</a>]
<b>On Behalf Of </b>Cyriac Kandoth<br>
<b>Sent:</b> Friday, May 22, 2015 3:21 PM<br>
<b>To:</b> Ensembl developers list<br>
<b>Cc:</b> Ahmet Zehir; Nikolaus D. Schultz; Wang, Qingguo/Sloan Kettering Institute<br>
<b>Subject:</b> Re: [ensembl-dev] VEP reporting HGVS format for an insertion without 3' shifting across tandem repeat<u></u><u></u></span></p>
</div><div><div class="h5">
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">Thanks. --shift_hgvs works in VEP v79, but note that it was not listed in the documentation:<u></u><u></u></p>
<div>
<p class="MsoNormal"><a href="http://mar2015.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic" target="_blank">http://mar2015.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic</a><u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">The annotation for the VCF variant below, changed from p.Ala771_Tyr772insTyrValMetAla to p.Tyr772_Ala775dup... and we prefer the latter. Thanks so much!<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">17 37880984 . A ATACGTGATGGCT . . .<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">~Cyriac<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Fri, May 22, 2015 at 11:51 AM, Sarah Hunt <<a href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>> wrote:<u></u><u></u></p>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Hi Cyriac,<br>
<br>
The --shift_hgvs option is available in v79, so do try it and let us know if the results are not what you expect.<br>
<br>
All the best,<br>
<br>
Sarah<u></u><u></u></p>
<div>
<p class="MsoNormal">On 22/05/2015 16:46, Cyriac Kandoth wrote:<u></u><u></u></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">Thanks very much Sarah. This is good to know. We're using VEP v79 in offline more, on command line, on GRCh37 loci. Do we need to update to v80, to be able to use the --shift-hgvs option?
<u></u><u></u></p>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Cheers!<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">~Cyriac<u></u><u></u></p>
</div>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On Fri, May 22, 2015 at 4:39 AM, Sarah Hunt <<a href="mailto:seh@ebi.ac.uk" target="_blank">seh@ebi.ac.uk</a>> wrote:<u></u><u></u></p>
<div>
<div>
<blockquote style="border:none;border-left:solid #cccccc 1.0pt;padding:0in 0in 0in 6.0pt;margin-left:4.8pt;margin-right:0in">
<div>
<p class="MsoNormal"><br>
Hi Cyriac,<br>
<br>
Thanks for the query - could you supply a bit more information?. Are you using VEP through the web site, REST or by command line? Is your data on GRCh37 or GRCh38?
<br>
<br>
Prior to e!80, non-shifted desriptions were our default and the --shift_hgvs option had to be selected when using the command line script to produce 3' shifted HGVS annotation. As of e!80, shifted descriptions will be the default and there will be a command
line option to turn them off. <br>
<br>
The GRCh38 website was updated to e!80 yesterday and the GRCh37 site will be updated shortly.<br>
<br>
Best wishes,<br>
<br>
Sarah <u></u><u></u></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<div>
<p class="MsoNormal">On 21/05/2015 20:29, Cyriac Kandoth wrote:<u></u><u></u></p>
</div>
</div>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<div>
<div>
<p class="MsoNormal">Here is a VCF-format example of an insertion within a tandem repeat region, that reports HGVSp = p.Ala771_Tyr772ins.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal">17 37880984 . A ATACGTGATGGCT . . .<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">HGVS, at least for deletions, states "the most 3' position possible is arbitrarily assigned to have been changed". This is different from the oft-used convention of "left-shifting" indels. So what's the correct solution here?<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">This one's pretty complicated and I'm still trying to get my head around it. But I would love to hear from someone who worked on implementing HGVS notations into VEP.<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">Thanks!<u></u><u></u></p>
</div>
<div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<p class="MsoNormal">~Cyriac<u></u><u></u></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
</div>
</div>
<pre>_______________________________________________<u></u><u></u></pre>
<pre>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><u></u><u></u></pre>
<pre>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</blockquote>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">
http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></p>
</blockquote>
</div>
</div>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><u></u> <u></u></p>
<pre>_______________________________________________<u></u><u></u></pre>
<pre>Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><u></u><u></u></pre>
<pre>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">http://lists.ensembl.org/mailman/listinfo/dev</a><u></u><u></u></pre>
<pre>Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></pre>
</div>
</div>
</blockquote>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">
http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><u></u><u></u></p>
</div>
<p class="MsoNormal"><u></u> <u></u></p>
</div>
</div></div></div>
<p></p>
<p>The information in this e-mail is intended only for the person to whom it is<br>
addressed. If you believe this e-mail was sent to you in error and the e-mail<br>
contains patient information, please contact the Partners Compliance HelpLine at<br>
<a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br>
but does not contain patient information, please contact the sender and properly<br>
dispose of the e-mail.</p></div>
<br>_______________________________________________<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/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>