Understanding VCF : 0/0 v 0/1 v 1/0 v 1/1 etc

Question

[bernardmcnamee]

I need to get up to speed as the IT person for a new project and I think it will help if I understand what's behind the data as all the resources are bound up in genetics concepts / language.

bcftools query -f '%ID\t%REF\t%ALT[\t%GT][\t%TGT]\n' ID_0298249.vcf.gz | head -1
rs9701055       C       T       0/0     C/C

If the C is the ref genome and the T is the sample genome, what is the 0/0 and C/C significance?

[Eugene A]

Not sure what do you mean by "significance", it is just notation for genotype (as far as you do have 2 copie of DNA in each cell). So both copies of the DNA in your example harbour reference variant which is C.

If the question was: how sure you are about the fact that you do not have a T in this position - you can not say it from current vcf. The reason is a lack any staticstic on mapping and variant colling steps (these fields depends on previouse data processing).

[Medhat]

ALT - alternate base(s): Comma separated list of alternate non-reference alleles. These alleles do not have to be called in any of the samples.

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

Answer 1

[swbarnes2]

If the C is the ref genome and the T is the sample genome, what is the 0/0 and C/C significance?

T is not the sample genome. Did you even bother to look up how vcf format works?