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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Will,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">That’s very helpful, thank you.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Kind regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Luke<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Will McLaren<br>
<b>Sent:</b> 28 July 2016 09:21<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] How does the web VEP HGVS annotator choose RefSeq transcripts?<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Luke,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">When the VEP uses RefSeq transcripts it is in fact using the reference genome sequence to generate its predictions. RefSeq transcript models are mapped to the reference genome and the sequence retrieved from those mapped coordinates is
used. This means that if a RefSeq differs from the genome, you may see unexpected results WRT to the RefSeq sequence. [1]<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Each mapped transcript is analysed independently, though you may have VEP choose only one to analyse using any of the --pick flags [2].<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hope that helps<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Will McLaren<o:p></o:p></p>
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<p class="MsoNormal">Ensembl Variation<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">[1] : <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#refseq">http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#refseq</a><o:p></o:p></p>
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<p class="MsoNormal">[2] : <a href="http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick">http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On 27 July 2016 at 21:42, Luke Goodsell <<a href="mailto:Luke.Goodsell@ogt.com" target="_blank">Luke.Goodsell@ogt.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Hi,
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Could you please let me know by what criteria the VEP HGVS annotator chooses RefSeq transcripts as a reference? Ie, how does it choose which of the intersecting
transcripts to use as the reference?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Kind regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black">Luke<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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