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,
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,