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.