[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,
Anja
(*)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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