SAMtools
Filtering by either QUAL or GQ resulted in monotonic decreases in genotype mismatch rates in the SAMtools SNP set (Fig. 3, S23-24). Increasing DP did improve mismatch rates over lower DP thresholds, although mismatch rates plateaued over higher values (Fig. 3, S25). As with the other callers, these three filtering metrics performed well and would be useful for filtering SNPs with further stringency, however, there may be diminishing returns when filtering by DP with SAMtools.