Figure 3
From: Variant calling in low-coverage whole genome sequencing of a Native American population sample
Frequency dependence of site finding. The fraction of variant sites found is dependent on both the frequency range of the variant, and the method used to call variants. The GATK Unified Genotyper in multisample mode finds more variants at all frequency ranges, but the disparity is most pronounced at the lowest frequencies, where the Unified Genotyper finds approximately 50% more variant sites than THUNDER. Single-sample Unified Genotyper calls follow a model that assumes a constant probability of finding any site in a single sample.