Fig. 2: Comparison of mismatch rates by genotype (A) and by site (B) between SNP callers at variable numbers of sites called. Mismatch rates were calculated as the number of mismatched parent-offspring genotype calls out of the total number of genotypes called (A) and as the number of sites with at least one mismatched parent-offspring genotype call out of the total number of sites (B). Variation in the number of sites called for a particular SNP caller was generated by additional incremental filtering to different degrees with depth, genotype quality, and quality score where applicable.