Question: What is phasing quality (PQ) and what does it mean?
Answer: PQ is a phred scaled probability that a heterozygous variant is phased wrong. PQ values greater than 27 are marked as phased by Long Ranger. A PQ score of 27 means that the algorithm thinks there is a probability of 0.002 that the phasing is wrong, or a 99.8% chance that it is right. This phasing is reflected in the genotype field (GT) in the sample column of the VCF file by a "|" in place of a "/". PQ values greater than 60 indicate that the algorithm has more support for the phasing decision. It is not, however, recommended to interpret these high PQ values directly as an error probability. In Loupe Bowser, all scores above 60 are treated as 60. For more information on PQ and other VCF flags please see our Phased VCF page.