Question: Question about genotype phased PQ and PS in VCF file format 4.1
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gravatar for Chen
3.5 years ago by
Chen910
Chen910 wrote:

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?

phased snp genotype vcf • 1.2k views
ADD COMMENTlink modified 3.5 years ago by mastal5112.0k • written 3.5 years ago by Chen910
0
gravatar for mastal511
3.5 years ago by
mastal5112.0k
mastal5112.0k wrote:

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/

ADD COMMENTlink written 3.5 years ago by mastal5112.0k
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