Table 3.

Somatic CNV calling performance comparison on 13 bladder cancer test samples from Guo et al.³¹

Tool	DEL Precision	DUP Precision	Overall Precision	DEL Recall	DUP Recall	Overall Recall	DEL F1 Score	DUP F1 Score	Overall F1 Score
XHMM	0.235	0.962	0.698	0.012	0.028	0.020	0.023	0.054	0.038
DECoNT-XHMM	0.193	0.950	0.572	0.010	0.023	0.017	0.019	0.045	0.033
ECOLE	0.373	0.673	0.523	0.019	0.010	0.015	0.036	0.020	0.029
ECOLEFT−SOMATIC	0.243	0.423	0.333	0.147	0.372	0.260	0.183	0.395	0.292

CNVnator calls are used as the semi-ground truth to calculate the metrics.