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Fig. 2 | Genome Biology

Fig. 2

From: Genotyping structural variants in pangenome graphs using the vg toolkit

Fig. 2

Structural variants from the HGSVC and Genome in a Bottle datasets. HGSVC: Simulated and real reads were used to genotype SVs and compared with the high-quality calls from Chaisson et al. [22]. Reads were simulated from the HG00514 individual. Using real reads, the three HG00514, HG00733, and NA19240 individuals were tested. GIAB: Real reads from the HG002 individual were used to genotype SVs and compared with the high-quality calls from the Genome in a Bottle consortium [21, 23, 25]. a Maximum F1 score for each method (color), across the whole genome or focusing on non-repeat regions (x-axis). We evaluated the ability to predict the presence of an SV (transparent bars) and the exact genotype (solid bars). Results are separated across panels by variant type: insertions and deletions. SVTyper cannot genotype insertions, hence the missing bars in the top panels. b Maximum F1 score for different size classes when evaluating on the presence of SVs across the whole genome. c Size distribution of SVs in the HGSVC and GIAB catalogs

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