Different symbols in genotype field in VCF files

Question

[khatami.mahshid]

Hello

I see frequently in my VCF file that in genotype instead of "0/0" or "0/1" or "1/0", there is ".:."

what does this ".:." symbol mean?

thanks a lot.

[williamsbrian5064]

I think that is a no-call. I have that issue when I have a low depth of coverage in that particular variant location

[Ram]

.:. is not the value for the GT field. Given that FORMAT is : separated, the GT value is just ., which is a no-call/unknown, like williamsbrian5064 says.