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<div>Hi Will,</div>
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<div>This helped a lot, thanks! And great to hear about the change for the next release.</div>
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<div>Cheers,</div>
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<div>Eva</div>
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<span style="font-weight:bold">From: </span>Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 11 February 2014 17:43<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] VEP script - per gene and canonical options<br>
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<div dir="ltr">Hello,
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<div>There is only one canonical transcript per gene.</div>
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<div>--per_gene picks the transcript that gives the most severe consequence type; no account is taken of whether the transcript is canonical. If two or more transcripts give the same consequence, the one chosen is essentially random - if this happens to be
the canonical one then it will be shown as such.</div>
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<div>This is being tweaked for the next release of VEP (75); priority is given to canonical then protein coding transcripts before consequence rank. There will be a new flag, --pick that picks one consequence per variant according to these criteria. --per_gene
will do the same, but will give one per gene if more than one gene is overlapped by the variant.</div>
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<div>Hope that helps</div>
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<div>Will McLaren</div>
<div>Ensembl Variation</div>
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<div class="gmail_quote">On 11 February 2014 16:31, Eva Goncalves Serra <span dir="ltr">
<<a href="mailto:egs@sanger.ac.uk" target="_blank">egs@sanger.ac.uk</a>></span> wrote:<br>
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<div>Hi,</div>
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<div>I am using VEP and the option —per_gene to output only the most severe consequence for a gene (the documentation says that the choice of transcript is arbitrary id more than one has the same predicted consequence) and also —canonical to denote whether
the transcript is the canonical one or not. </div>
<div>My question is: if using these two options together, is the -canonical option relative to the transcript chosen with the most severe consequence by the –per_gene option?</div>
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<div>Thanks a lot,</div>
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<div>Eva</div>
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<div>PhD Student, Wellcome Trust Sanger Institute</div>
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