[ensembl-dev] VEP run on chrY

[Will McLaren]

Hi Yuan,

VEP shouldn't change the genotype data in your VCF file, can you provide a
sample of input and a command that recreates the issue?

Regards

Will

On 22 July 2015 at 09:41, Yuan Chen <yuan at sanger.ac.uk> wrote:

> Hi Will,
>
> When I run VEP (79 version) on chrY which has genotype 0 or 1 in vcf file
> (i.e not 0/0), the VEP output file changed all 0 to '.', is this expected ?
>
> yuan
>
> Sent from my Huawei Mobile
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