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GT tag in VCF spec

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

gt vcf tags valid
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written by Jackie Jackie

Thank you very much. This is helpful!

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written by Jackie Jackie

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.

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written by WouterDeCoster WouterDeCoster

1 answer

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 . . .
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written by Pierre Lindenbaum Pierre Lindenbaum

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