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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Dear ensembl developers,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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><o:p> </o:p></p><p class=MsoNormal>17 21204210 21204210 C/T<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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><o:p> </o:p></p><p class=MsoNormal><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=xasvH54pdz3W0DvS</a><o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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><o:p> </o:p></p><p class=MsoNormal><a href="http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV">http://grch37.ensembl.org/Homo_sapiens/Tools/VEP/Ticket?tl=s8tIqV5q7NEtd4wV</a> <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>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><o:p> </o:p></p><p class=MsoNormal>An answer to a previous question suggests that this is possible. Could you please advise?<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><a href="http://lists.ensembl.org/pipermail/dev/2011-May/006173.html">http://lists.ensembl.org/pipermail/dev/2011-May/006173.html</a> <o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Many thanks in advance,<o:p></o:p></p><p class=MsoNormal>David <o:p></o:p></p></div></body></html>