[ensembl-dev] VEP - Annotation of Biallelic VCFs

Anja Thormann anja at ebi.ac.uk
Mon Apr 27 18:18:59 BST 2020

Dear Margret,

if you want to annotate genotype data you need to use the individual(*) option. VEP will annotate only alternate alleles that are present in the genotypes of the specified individuals.

Best regards,

(*)https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_individual <https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_individual>

> On 24 Apr 2020, at 22:16, Linan, Margaret <margaret.linan at mssm.edu> wrote:
> Hi – 
> How does VEP handle VCFs with biallelic variants?  Do you recommend any command line options for this type of data?
> Best,
> Margaret 
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