Question

GT tag in VCF spec

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7.1 years ago

Jackie ▴ 70

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 • 1.5k views

ADD COMMENT • link 7.1 years ago by Jackie ▴ 70

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Thank you very much. This is helpful!

ADD REPLY • link 7.1 years ago by Jackie ▴ 70

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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.

ADD REPLY • link 7.1 years ago by WouterDeCoster 47k

score 4 · Accepted Answer · 2017-03-15

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 . . .