[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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