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Genotype (GT)

Hi all :)

I have some doubts regarding the genotype.
I don't understand: sample_AF is reflecting the GT, is it correct? I mean if AF is around 0,5 GT should be 0/1 and if AF is around 1 GT is 1/1.
So if I have low AF, for example 0,094 or 0,1, the GT should be 0/0, is it correct?
The problem is that sometime with a low AF I have GTs as 0/1 or 1 (e.g AF (0,094) - GT 0/1 or....AF (0,13) - GT 1/1). Is it reliable for my analysis? (GQ is 99)

Could you help me to understand how genotype is calculated, please?
Thank you,


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin
    edited April 2019

    Hi @valirilla

    Please post records of vcf corresponding to your questions.
    Also what tool did you use to generate the vcf? Please post the exact command you used and the version of the tool.

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