<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=utf-8"><meta name=Generator content="Microsoft Word 14 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Thanks for that Will,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>I thought this might have been the case for this variant, but let’s say we have a variant that is co-located with a ‘passed QC’ (same allele) dbSNP variant and a HGMD variant. <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>My understanding is that VEP (with –check-existing, --check-alleles) would report the co-located variant but not the HGMD variant because it cannot check the HGMD allele. Is it possible to overwrite the check allele for HGMD (or sources that have no allele information) and hence report both the matched allele dbSNP and HGMD entry? I understand that –check-alleles is only doing its job.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Here is an example, VEP (--check-existing & --check-alleles):<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>VEP (--check-existing only):<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ</a><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>Regards,<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'>David<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'>From:</span></b><span lang=EN-US style='font-size:10.0pt;font-family:"Tahoma","sans-serif"'> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org] <b>On Behalf Of </b>Will McLaren<br><b>Sent:</b> 13 May 2015 11:28<br><b>To:</b> Ensembl developers list<br><b>Subject:</b> Re: [ensembl-dev] HDMG/dbSNP co-located variants<o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>Hi David,<o:p></o:p></p><div><p class=MsoNormal><br>The dbSNP variant in question has been flagged by our QC pipeline as failed (actually in this case by dbSNP; we also include their QC flags).<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal><a href="http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs55796947">http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs55796947</a><o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Flagged variants are not included in the VEP output by default; to include them, add "--failed 1" to your command line.<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Regards<o:p></o:p></p></div><div><p class=MsoNormal><o:p> </o:p></p></div><div><p class=MsoNormal>Will McLaren<o:p></o:p></p></div><div><p class=MsoNormal>Ensembl Variation<o:p></o:p></p></div></div><div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal>On 11 May 2015 at 12:39, David Blaney <<a href="mailto:David.Blaney@ogt.com" target="_blank">David.Blaney@ogt.com</a>> wrote:<o:p></o:p></p><div><div><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Dear ensembl developers,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I am trying to annotate the following variant using the GRCh37 online VEP tools and have a couple of questions regarding the ‘Existing Variation’ column.<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>17 21204210 21204210 C/T<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>When I run VEP using the with the defaults parameters (in particular with the –check-existing flag selected and the –check-alleles flag not selected) there is a HGMD identifier in the ‘Exisitng Variation’ column which is great! Please see the ticket here:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS" target="_blank">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS</a><o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>When I run VEP using the with the parameters –check-existing flag selected and the –check-alleles flag selected, there is no ‘Existing Variation’ reported, despite the fact that the variant is co-located with a dbSNP variant that has the correct alleles. Ticket here:<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV" target="_blank">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV</a> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>I understand that it is not possible to match the allele for HDMG as you do not have that information but is there a way I can configure VEP to report both HGMD ID and the co-located, matched allele, dbSNP variant. <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>An answer to a previous question suggests that this is possible. Could you please advise?<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><a href="http://lists.ensembl.org/pipermail/dev/2011-May/006173.html" target="_blank">http://lists.ensembl.org/pipermail/dev/2011-May/006173.html</a> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'> <o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>Many thanks in advance,<o:p></o:p></p><p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'>David <o:p></o:p></p></div></div><p class=MsoNormal style='margin-bottom:12.0pt'><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" 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><o:p></o:p></p></div><p class=MsoNormal><o:p> </o:p></p></div></div></body></html>