<span id="mailbox-conversation"><div>Awesome, thanks for this!</div>
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<div>(and for pointing me to the destroy subroutine)</div></span><div class="mailbox_signature">
<br>-Konrad</div>
<br><br><div class="gmail_quote"><p>On Thu, May 28, 2015 at 8:56 AM, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br></p><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><div>
<div dir="ltr">Hi again Konrad,<div><br></div>
<div>I added in a flag for release 80, --minimal, see <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_minimal">http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_minimal</a>
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<div>Note the caveats that reported coordinates etc may get screwed up (they shouldn't if you use VCF output), but if you use VCF in and out and --allele_number you should be able to keep track of everything OK.</div>
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<div>HTH</div>
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<div>Will</div>
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<br><div class="gmail_quote">On 16 April 2015 at 15:43, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<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>
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<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>
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<div>Regards</div>
<div><br></div>
<div>Will</div>
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<div><div class="h5">On 16 April 2015 at 05:30, Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org">konradk@broadinstitute.org</a>></span> wrote:<br></div></div>
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<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>
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<div>1       3394415 .       CGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT      TGCCTCCCGGCTCTGTCCCCCCAGTCCCTCCCACTGATCTCT,C    9533.30 PASS</div>
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<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">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>
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<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><font color="#888888"><br>-Konrad</font></span>
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