Question about genotype phased PQ and PS in VCF file format 4.1

Question

[Chen Sun]

In VCF file format 4.1,

genotype has two conditions unphased and phased.

What does it mean phased or unphased? Does it mean that PQ( phasing quality) is calculated or not?

And can anyone give an example about PS (phase set)? Because I tried many variant calling tools but fail to get any PS information, what would PS info looks like?

Answer 1

[mastal511]

According to the VCF format 4.1 and 4.3 specifications, it sounds like they haven't decided on a specified way of defning PQ, so the PQ tag is reserved for future use. So phased/unphased doesn't refer to whether or not PQ has been calculated.

PS is supposed to be a 32-bit integer.

This article may help to explain what phased means in relation to genotypes. http://www.chromosomechronicles.com/2009/09/08/phasing-determining-which-snps-are-inherited-together/