[ensembl-dev] VEP vcf annotation

Dietmar Rieder dietmar.rieder at i-med.ac.at
Fri Jul 2 10:52:02 BST 2021


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

-- 
_________________________________________
D i e t m a r  R i e d e r, Mag.Dr.
Head of HPC/Bioinformatics facility
Innsbruck Medical University
Biocenter - Institute of Bioinformatics
Innrain 80, 6020 Innsbruck
Phone: +43 512 9003 71402
Fax: +43 512 9003 73100
Email: dietmar.rieder at i-med.ac.at
Web:   http://www.icbi.at


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