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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Sarah,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Indeed, that would be very helpful.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Kind regards,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Luke</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Dev <dev-bounces@ensembl.org> on behalf of Sarah Hunt <seh@ebi.ac.uk><br>
<b>Reply-To: </b>Ensembl developers list <dev@ensembl.org><br>
<b>Date: </b>Monday, 11 December 2017 at 15:16<br>
<b>To: </b>Ensembl developers list <dev@ensembl.org><br>
<b>Subject: </b>Re: [ensembl-dev] VEP e!90 HGVS del/dup bases removed?<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
Hi Luke,<br>
<br>
We don't have a thread to share for this one. If the deleted reference allele used was reported seperately, would this be adequate for your checks?
<br>
<br>
Sarah<o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/12/2017 14:01, Luke Goodsell wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal"><span style="font-size:11.0pt">Hi Sarah,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Thanks for providing an answer so quickly.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Is there a thread I can read through where this change was discussed? I’d like to better understand the rationale for discarding the bases rather than having them, say, optionally removed. Just because they
aren’t canonical or perfect in all situations doesn’t mean they aren’t useful in some situations.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Kind regards,</span><o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Luke</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Dev
<a href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> on behalf of Sarah Hunt
<a href="mailto:seh@ebi.ac.uk"><seh@ebi.ac.uk></a><br>
<b>Reply-To: </b>Ensembl developers list <a href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
<b>Date: </b>Monday, 11 December 2017 at 13:44<br>
<b>To: </b>Ensembl developers list <a href="mailto:dev@ensembl.org"><dev@ensembl.org></a><br>
<b>Subject: </b>Re: [ensembl-dev] VEP e!90 HGVS del/dup bases removed?</span><o:p></o:p></p>
</div>
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<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
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<p> <o:p></o:p></p>
<p>Hi Luke,<o:p></o:p></p>
<p>After discussions with collaborators on the myriad of different ways the same allele can be represented in HGVS, we removed the deleted/duplicated bases to conform with the recommended rather than permitted version of the nomenclature. There isn't a way
to include them at the moment. This could be added, but it would contribute to the difficulty in comparing annotations across different sources.<o:p></o:p></p>
<p>Best wishes,<o:p></o:p></p>
<p>Sarah<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div>
<p class="MsoNormal">On 11/12/2017 13:18, Luke Goodsell wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">We’ve noticed since upgrading from e!88 to e!90 that the deleted/duplicated bases are no longer being reported in HGVS strings. Is there a way to include them?</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Out of curiosity, why were they removed? It was my understanding that they are not required by the HGVS spec, but that they can be optionally included. We use them downstream as a way to double-check the variant
annotation.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Kind regards,</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;color:black">Luke</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt">This e-mail message contains confidential information intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, please do not disseminate, distribute
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