Genotype Quality for Variant and Nonvariant Sites

The gVCF file uses an adapted version of genotype quality for variant and nonvariant site filtration. This value is associated with the key GQX. The GQX value is intended to represent the minimum of {Phred genotype quality assuming the site is variant, Phred genotype quality assuming the site is nonvariant}. The reason for using this value is to allow a single value to be used as the primary quality filter for both variant and nonvariant sites. Filtering on this value corresponds to a conservative assumption appropriate for applications where reference genotype calls must be determined at the same stringency as variant genotypes, ie: