1000 genome project - difference between "0" and "0|0"

Question

[mbk0asis]

Hi, all!

I'm analyzing variants in a gene of interest and found some variants were denoted as "0" or "0|0" by samples.

I'm guessing "0" would mean no sequencing while "0|0" indicates homozygous WT.

Am I on the right track? What are those marks mean?

Thank you!

Answer 1

[Santosh Anand]

From VFC Manual

https://samtools.github.io/hts-specs/VCFv4.1.pdf

• GT : genotype, encoded as allele values separated by either of / or |. The allele values are 0 for the reference allele (what is in the REF field), 1 for the first allele listed in ALT, 2 for the second allele list in ALT and so on. For diploid calls examples could be 0/1, 1|0, or 1/2, etc. For haploid calls, e.g. on Y, male nonpseudoautosomal X, or mitochondrion, only one allele value should be given; a triploid call might look like 0/0/1. If a call cannot be made for a sample at a given locus, ‘.’ should be specified for each missing allele in the GT field (for example ‘./.’ for a diploid genotype and ‘.’ for haploid genotype). The meanings of the separators are as follows (see the PS field below for more details on incorporating phasing information into the genotypes): ◦ / : genotype unphased ◦ | : genotype phased

[mbk0asis]

So, "0" = males, "0|0" = females for chrX genes?

[Santosh Anand]

Yes, except for the mitochondrial DNA and PAR regions, https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2435358/

[mbk0asis]

Thank you! I understood :)