<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Hi João,<br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">VEP trims alleles if the substitution is unbalanced (typically an insertion or deletion where the length(REF) != length(ALT)), and by default only trims the first base from each.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">You may force VEP to fully strip each pair of alleles using --minimal [1]; using this flag I get missense as expected.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">We’re currently working on expanding and clarifying the documentation for this, with the update available in release 90.</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Regards</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Will McLaren</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">Ensembl Variation</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px; color: rgba(0,0,0,1.0); margin: 0px; line-height: auto;">[1] : http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_minimal</div> <div id="bloop_sign_1500027084125395968" class="bloop_sign"></div> <br><p class="airmail_on">On 14 July 2017 at 11:03:40, João Eiras (<a href="mailto:joao.eiras@gmail.com">joao.eiras@gmail.com</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>Hi.
<br>
<br>I stumbled upon COSMIC annotation COSM366465
<br>http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=366465
<br>
<br>The annotations is in the VCF as
<br>
<br>chr4 46977409 COSM366465 CCT CAT
<br>
<br>VEP annotates this as (splice_region_variant,coding_sequence_variant)
<br>over transcript ENST00000264318. This transcript is in the reverse tr
<br>
<br>However, this is actually a SNP in the last nucleotide.
<br>
<br>The variant can be stripped as
<br>
<br>chr4 46977410 COSM366465 C A
<br>
<br>and in this case VEP does annotate it as a missense_variant.
<br>
<br>Without looking at the code, my guess is that VEP strips the common
<br>nucleotides of he tips of REF and ALT from the left in case of a
<br>forward strand transcript, and right side in case of a backward strand
<br>transcript. So, the left most C remains there and VEP thinks that
<br>nucleotide is changed.
<br>
<br>Am I missing something ?
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<br></div></div></span></blockquote></body></html>