Fig. 1

Structural variation in vg. a vg uses the read coverage over possible paths to genotype variants in a snarl. The cartoon depicts the case of a heterozygous insertion and a homozygous deletion. The algorithm is described in detail in “Methods.” b Simulation experiment. Each subplot shows a comparison of genotyping accuracy for five methods. Results are separated between types of variation (insertions, deletions, and inversions). The experiments were also repeated with small random errors introduced to the VCF to simulate breakpoint uncertainty. For each experiment, the x-axis is the simulated read depth and the y-axis shows the maximum F1 across different minimum quality thresholds. SVTyper cannot genotype insertions, hence the missing line in the top panels