Figure 2.

Screenshot of the output summary metrics of RTGtools

“Threshold” represents the genotyping quality (GQ) threshold, and you can refer to the row where the threshold is “None”. “baseline” represents the true data, and “call” represents the GATK callset. Therefore, “True-pos-baseline” means baseline variants that match between the baseline and calls; “True-pos-call” means called variants that match between the baseline and calls; “False-pos” means called variants not matched in the baseline; “False-neg” means baseline variants not matched in the call set. “Precision” means the precision rate of called variants; “Sensitivity” means the recall rate of baseline variants; “F-measure” means the weighted harmonic mean of its precision and sensitivity.