FreeBayes
Increasing stringency in either of DP or GQ resulted in monotonically decreasing genotype mismatch rates in the FreeBayes SNP set (Fig. 3, S11-12). Similarly, increasing QUAL over lower values decreased the mismatch rate, however, mismatch rates did plateau over very high QUAL values (Fig. S13). All three filtering metrics performed well on our dataset and would be useful metrics to filter SNPs with increased stringency.