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 | – | – | – | – |