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<p>Hi Dietmar,</p>
<p>I'm unable to reproduce the issue. Could you please send me the
VEP command you are running? <br>
</p>
<p><br>
</p>
<p>Thanks</p>
<p>Diana <br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 02/07/2021 10:52, Dietmar Rieder
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20210702095311.C53F21197F1_DEE207B@hh-mx4.ebi.ac.uk">Hi,
<br>
<br>
we are using VEP (103) to annotat our VCFs and we just stumbled
over the situation that for the mutation chr5_112838250_C/T
(chr5:112838250) we get 7 annotated transcript variants in the
gene with SYMBOL ACP and one in the "gene" with SYMBOL AC008575.1,
in the VEP txt output, which is fine.
<br>
<br>
BUT
<br>
<br>
when we use -vcf to get an annotated vcf file we get the mutation
on that position only annotated with the SYMBOL AC008575.1
<br>
This is problematic, because the canonical gene here is APC (a
known driver gene in CRC) and we miss it when parsing the VCF
<br>
<br>
Would it be possible to add all gene symbols to the SYMBOL field
in the CSQ of the vcf?
<br>
<br>
Thanks
<br>
Dietmar
<br>
<br>
<br>
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