Different symbols in genotype field in VCF files
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.
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khatami.mahshid •
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I think that is a no-call. I have that issue when I have a low depth of coverage in that particular variant location
.:.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.