<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi David,<div class=""><br class=""></div><div class="">It should be possible to make special case exceptions, yes.</div><div class=""><br class=""></div><div class="">I’ll look into adding this for the next VEP release.</div><div class=""><br class=""></div><div class="">Regards</div><div class=""><br class=""></div><div class="">Will</div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 13 May 2015, at 14:24, David Blaney <<a href="mailto:David.Blaney@ogt.com" class="">David.Blaney@ogt.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks for that Will,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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.<span class="Apple-converted-space"> </span><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">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 class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Here is an example, VEP (--check-existing & --check-alleles):<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ" style="color: purple; text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ</a><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">VEP (--check-existing only):<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ" style="color: purple; text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=m7LvOEu93tqyLdsQ</a><o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Regards,<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">David<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><b class=""><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 10pt; font-family: Tahoma, sans-serif;" class=""><span class="Apple-converted-space"> </span><a href="mailto:dev-bounces@ensembl.org" class="">dev-bounces@ensembl.org</a> [<a href="mailto:dev-bounces@ensembl.org" class="">mailto:dev-bounces@ensembl.org</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Will McLaren<br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>13 May 2015 11:28<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Ensembl developers list<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] HDMG/dbSNP co-located variants<o:p class=""></o:p></span></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Hi David,<o:p class=""></o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><br class="">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 class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs55796947" style="color: purple; text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?v=rs55796947</a><o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Flagged variants are not included in the VEP output by default; to include them, add "--failed 1" to your command line.<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Regards<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Will McLaren<o:p class=""></o:p></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Ensembl Variation<o:p class=""></o:p></div></div></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><o:p class=""> </o:p></div><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">On 11 May 2015 at 12:39, David Blaney <<a href="mailto:David.Blaney@ogt.com" target="_blank" style="color: purple; text-decoration: underline;" class="">David.Blaney@ogt.com</a>> wrote:<o:p class=""></o:p></div><div class=""><div class=""><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Dear ensembl developers,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">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 class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">17 21204210 21204210 C/T<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">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 class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS" target="_blank" style="color: purple; text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS</a><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">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 class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV" target="_blank" style="color: purple; text-decoration: underline;" class="">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV</a><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">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.<span class="Apple-converted-space"> </span><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">An answer to a previous question suggests that this is possible. Could you please advise?<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""><a href="http://lists.ensembl.org/pipermail/dev/2011-May/006173.html" target="_blank" style="color: purple; text-decoration: underline;" class="">http://lists.ensembl.org/pipermail/dev/2011-May/006173.html</a><o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class=""> <o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">Many thanks in advance,<o:p class=""></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">David<span class="Apple-converted-space"> </span><o:p class=""></o:p></div></div></div><p class="MsoNormal" style="margin: 0cm 0cm 12pt; 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