[ensembl-dev] VEP vcf annotation

Diana Lemos dlemos at ebi.ac.uk
Fri Jul 2 11:18:30 BST 2021


Hi Dietmar,

I'm unable to reproduce the issue. Could you please send me the VEP 
command you are running?


Thanks

Diana


On 02/07/2021 10:52, Dietmar Rieder wrote:
> Hi,
>
> 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.
>
> BUT
>
> when we use -vcf to get an annotated vcf file we get the mutation on 
> that position only annotated with the SYMBOL AC008575.1
> This is problematic, because the canonical gene here is APC (a known 
> driver gene in CRC) and we miss it when parsing the VCF
>
> Would it be possible to add all gene symbols to the SYMBOL field in 
> the CSQ of the vcf?
>
> Thanks
>   Dietmar
>
>
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