[ensembl-dev] VEP - Annotation of Biallelic VCFs

[Nicolas Thierry-Mieg]

Hello,

depending on what problem you are trying to solve, --allele_number might 
also help:
https://lists.ensembl.org/pipermail/dev_ensembl.org/2017-June/012503.html

Regards,
Nicolas


On 4/27/20 7:18 PM, Anja Thormann wrote:
> 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
> 
>> On 24 Apr 2020, at 22:16, Linan, Margaret <margaret.linan at mssm.edu 
>> <mailto: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