Table 1. Parameter settings for VarScan comparisons.

Unless a p-value cutoff is specified, VarScan doesn’t calculate p-values.

	VarScan-Default	VarScan-p-value	VarScan-Cons
Minimum coverage	8	8	10
Minimum supporting reads	2	2	4
Minimum average quality	15	15	20
Minimum variant frequency	0.01	0.01	0.3
Maximum p-value	(none)	0.05	(none)