VarScan
Increasing stringency in DP or increasing stringency in GQ beyond 20 produced appreciable improvements in genotype mismatch rate in the VarScan SNP set (Fig. 3, S35-36). Similar to SAMtools, filtering by DP resulted in mismatch rates plateauing over higher values (Fig. S35). Both DP and GQ appear to be useful for increased filtering with VarScan, however, there may be diminishing returns when filtering by DP with VarScan.