Table 4.

SNP genotyping precision and recall for confident regions as reported by hap.py in the human chromosome 1 experiment

Workflow	Precision	Recall
Baseline/GATK	99.73%	99.71%
Baseline/BCFtools	99.76%	99.30%
PanVC/GATK	99.62%	99.73%
PanVC/BCFtools	99.58%	99.48%
GraphTyper 2	99.86%	95.56%
vg/GATK	99.30%	96.74%
vg/BCFtools	99.58%	95.90%

Note: Only variants passing all filters were considered.