Fig. 2

Each dot represents an arithmetic mean of recall (X-axis) and precision (Y-axis) for one pipeline configuration calculated based on repeated random sub-sampling of 3 input datasets (220 samples). The crosshair lines show the standard deviation of the respective results across the sub-sampled sets. Individual variant callers (Mutect2, VarDict and VarScan2) are colour coded with a distinguished default setting for each. The default settings and the best performing configurations for each variant caller are also enlarged. Based on our experiment, the largest variant calling improvement (2.36× higher F-measure compared to default settings, highlighted by an arrow) and also the highest overall recall, precision, precision-recall, and F-measure were registered for VarScan2. In case of VarDict, a significant improvement in variant detection, mainly for recall (2.42×) was observed. The optimization effect on Mutect2 had a great effect on increasing the precision (1.74×). Although the F-measure after optimization did not reach as high values as VarScan2 and VarDict, Mutect2’s default setting provided the best results, mainly in a sense of recall