Table 1.

Various parameters along with their default values defined in each mutation caller

Option	MuTect2	VarScan2	SAMtools	VarDict	Pisces
Threshold for allele frequency	–	0.01	–	0.05	0.01
Base quality score threshold	18	–	–	–	–
Max base quality score	–	–	–	–	100
Min map quality	20	null	0	null	1
Mean map quality	–	null	–	null	–
Max map quality	null	–	–	–	–
Min coverage	–	8	–	–	10
Max coverage	–	–	250	–	–
Min supporting variant reads	–	2	–	–	–
Min variant quality score	–	–	–	–	20
Strand bias filter	–	–	–	–	0.5
Min reads to strand bias	2	–	–	–	–

A dash means that the corresponding parameter was not defined in the caller’s settings