Table 5.

Definition of variant calling performance metrics. TP, TN, FP, FN are true positive, true negative, false positive, false negative respectively.

Metric	Synonym	Formula	Relation with other metrics
Sensitivity	Recall	$\frac{TP}{TP+FN}$
Specificity		$\frac{TN}{TN+FP}$
False positive rate (FPR)		$\frac{FP}{TN+FP}$	1 - specificity
Positive predictive value (PPV)	Precision	$\frac{TP}{TP+FP}$
False discovery rate (FDR)		$\frac{FP}{TP+FP}$	1 - PPV
F-score	F1 score	$2\times \frac{\text{sensitivity}\times \text{PPV}}{\text{sensitivity}+\text{PPV}}$	harmonic mean of sensitivity and PPV