<div dir="ltr">Hi Konrad,<div><br></div><div>Thanks for finding this.<br></div><div><br></div><div>We'll look into a solution, though as it will involve significant code refactoring, it won't be available until (at the earliest) the next VEP/Ensembl release (80, due some time next month).</div><div><br></div><div>In the short term you could break out the variant onto separate VCF lines, though I appreciate that introduces difficulties with individual-level data.</div><div><br></div><div>Regards</div><div><br></div><div>Will</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 16 April 2015 at 05:30, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Will, VEP folk,<div><br></div><div>Unfortunately, allele representation has bit us once again. We have the following variant:</div><div><br></div><div>1       3394415 .       CGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT      TGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT,C    9533.30 PASS</div><div><br></div><div>Which is really a SNV that overlaps a larger deletion. VEP reads this as CGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT-> TGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT and since that sequence overlaps a splice acceptor (e.g. ENST00000378373), it marks it as a splice_acceptor_variant (even though it doesn't change the acceptor site - just tried VEP v79 on GRCh37 and same issue). Ideally, we'd put this through minimal representation (as we have implemented here: <a href="https://github.com/ericminikel/minimal_representation" target="_blank">https://github.com/ericminikel/minimal_representation</a> which nicely cuts the alleles down), but unfortunately inside a multi-sample VCF, this doesn't really work. Is there a way for this to happen inside VEP/is there a fix to this?<br><div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word"><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px"><br></div><div style="color:rgb(0,0,0);font-family:Helvetica;font-size:12px;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">Thanks!<span class="HOEnZb"><font color="#888888"><br>-Konrad</font></span></div></div></div></div></div><br>_______________________________________________<br>
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