GT tag in VCF spec

Question

[Jackie]

Hi,

Is GT tag in the FORMAT col a required tag by VCF spec? If a VCF does not have GT tag, is it still a valid VCF? Or put it another way, what is the minimum information that makes a VCF valid?

Thanks

[Jackie]

Thank you very much. This is helpful!

[WouterDeCoster]

Please use ADD COMMENT to reply to earlier answers, as such this thread remains logically structured and easy to follow. I now moved your reaction but as you can see it's not optimal.

If the answer from Pierre resolved your question you should mark it as accepted.

Answer 1

[Pierre Lindenbaum]

if a VCF does not have GT tag, is it still a valid VCF?

https://samtools.github.io/hts-specs/VCFv4.2.pdf

The first sub-field must always be the genotype (GT) if it is present.

NO: GT is not required.

what is the minimum information that makes a VCF valid?

just a VCF header.... :-)

##fileformat=VCFv4.2
#CHROM POS ID REF ALT QUAL FILTER INFO
1 2 . N N . . .