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Table 1 Various parameters along with their default values defined in each mutation caller

From: Accuracy and reproducibility of somatic point mutation calling in clinical-type targeted sequencing data

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