Figure 3
From: Empirical evaluation of variant calling accuracy using ultra-deep whole-genome sequencing data
Definition of the genotype concordance measurement. (A) Genotype concordance matrix. All combinations of the three SNV genotypes (reference / reference [Ref/Ref], reference / alterative [Ref/Alt], alternative / alternative [Alt/Alt]) between the WGS and SNP microarray were assigned. The positions were classified as false positive when alternate alleles were discordant between the sequence and the microarray data. We assessed genotypes as homo-reference that were not included in the VCF files of the WGS data. (B) Genotype concordance metrics. We adopted all the genotypes on the microarray as a parameter during assessment of CR, FPR, and FNR, whereas variants called in each of the WGS data were used to assess NTPR.
