Different symbols in genotype field in VCF files
0
0
Entering edit mode
3.3 years ago

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.

gene SNP • 552 views
ADD COMMENT
2
Entering edit mode

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

ADD REPLY
1
Entering edit mode

.:. 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.

ADD REPLY

Login before adding your answer.

Traffic: 2006 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6