All concordant and discordant genotyped variants were analyzed for genotyping quality metrics provided in the VCF files and GenomeStudio report files for WGS and BeadChip genotyping, respectively. The following quality metrics obtained via WGS genotyping pipeline were analyzed: DP variant read depth at a particular position for a particular sample.QUAL Phred-scaled quality score for the assertion made in ALT. i.e., −10log10(Pcall in ALT is wrong), if ALT is “.” (no variant) then this is –10log10(Pvariant), and if ALT is not “.” this is –10log10(Pno variant).RGQ unconditional reference genotype confidence, encoded as a Phred quality –10log10(Pgenotype call is wrong).GQ conditional genotype quality, encoded as a Phred quality –10log10(Pgenotype call is wrong), conditioned on the site is variant.
