Fig. 2

Comparison of the genotype concordance, non-reference sensitivity, non-reference genotype concordance and precision of GATK, freebayes and SAMtools over various minor allele frequency bins. SNPs were binned into 100 groups according to their array-derived MAF. The mean of each metric was calculated within each minor allele frequency bin. The statistics of different genotype concordance metrics were measured according to Linderman et.al [20]. The orange squares represent variant caller GATK. The green circles stand for variant caller freebayes. The blue triangles stand for variant caller SAMtools