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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<br>
<br>
<div class="moz-cite-prefix">On 11/12/2017 14:01, Luke Goodsell
wrote:<br>
</div>
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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">Thanks for
providing an answer so quickly.<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">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.<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>
</div>
<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 <a class="moz-txt-link-rfc2396E" href="mailto:dev-bounces@ensembl.org"><dev-bounces@ensembl.org></a> on
behalf of Sarah Hunt <a class="moz-txt-link-rfc2396E" href="mailto:seh@ebi.ac.uk"><seh@ebi.ac.uk></a><br>
<b>Reply-To: </b>Ensembl developers list
<a class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><dev@ensembl.org></a><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>
</div>
<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>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<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>
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