Fig. 3

Genotyping accuracy of variant calls validated with sequencing reads and Mendelian relationships. a Filtering rate of heterozygous (0/1) and homozygous alternate (1/1) variant calls post-imputation for GATK and DV. Higher filtering rate indicates the genotype/allele is not consistent with k-mers from the same-sample sequencing reads. b Mendelian violation rate for 206 separate samples, with either 2 family members (Duo) or all 3 (Trio). Mendelian violations are defined as genotypes in the offspring that could not have been inherited from the parents. In the case of duos, only variants homozygous in the parent can be confirmed as violations of Mendelian inheritance