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.