What is genotype quality scale?

Question

[agata88]

Hi all!

I would like to ask what is the scale of genotype quality?

I've red that GATK still annotate variants with GQ 1-99. I have results from VarScan which shows me GQ from 1-255.

I am little confused, Is variant with GQ 255 as quality high as with 99? How about variant with GQ = 60 (1-255) and 60 (1-99)?

What is the difference between those two?

Thanks in advance,

Best,

Agata