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<p>Hi Oliver,</p>
<p>Thanks for reporting this issue.</p>
<p>We are looking into it - I'll let you know when we know more.</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Diana <br>
</p>
<p><br>
</p>
<p><br>
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<div class="moz-cite-prefix">On 26/07/2023 13:27, Oliver Langenhorn
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+rmU6-es-RCa9fW_0dZ6zDfwxVd2N8pCK_j9nSBFdRuhDWC6Q@mail.gmail.com">
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<div dir="ltr">Hi,
<div><br>
</div>
<div>I am trying to annotate a list of mutations in coding
HGVS notation with VEP, most of them go through pretty ok,
but some are creating troubles. One example is <span
style="color:rgb(51,51,51);font-family:"Luxi
Sans",Helvetica,Arial,Geneva,sans-serif;font-size:12.8px">TP53:c.110_120delinsC,
here's the job output: </span><a
href="https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=fbegKEYtZPdXtACp-9377859"
moz-do-not-send="true" class="moz-txt-link-freetext">https://www.ensembl.org/Homo_sapiens/Tools/VEP/Results?tl=fbegKEYtZPdXtACp-9377859</a></div>
<div><br>
</div>
<div>And that's the relevant part from the VCF:</div>
<div>17 7676249 TP53:c.110_120delinsC CCATTGCTTGG C . .</div>
<div>
<div>
<div><br>
</div>
<div>Whenever i try to use the generated VCF downstream,
there are issues because sequence starting at
17:7676249 in GRCh38 isn't actually <b>C</b>CATTGCTTGG
like in VEP-generated VCF. It is shorter: CATTGCTTGG,
see that here:</div>
<div><a
href="https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7676249-7676259"
target="_blank" moz-do-not-send="true"
class="moz-txt-link-freetext">https://www.ensembl.org/Homo_sapiens/Location/View?r=17:7676249-7676259</a><br>
</div>
<div><br>
</div>
<div>And so there's a reference mismatch. I am missing
something obvious?</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Oliver</div>
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