Mismatch Rates
With the additional incremental filtering, all callers dramatically improved in by-site mismatch rates and by-genotype mismatch rates, with the exception of VarScan which remained rather insensitive (Table S6; Fig. 2). UnifiedGenotyper, HaplotypeCaller, and SAMtools all showed striking improvements in mismatch rates with additional incremental filtering until about the 105.5 SNP mark, where mismatch rates for all three callers approached relative plateaus. FreeBayes showed continued improvements in mismatch rates with increased filtering and did not reach a point of diminishing returns. In contrast, VarScan did not substantially improve in mismatch rates with increased filtering, however, because VarScan called relatively few SNPs, minimal additional filtering could be applied. After additional incremental filtering to a specific number of sites called, UnifiedGenotyper consistently had the lowest genotype mismatch rate, followed by HaplotypeCaller, VarScan, SAMtools, and FreeBayes (Fig. 2A). The number of SNPs called (i.e., the degree of filtering applied) did not change the ranking of the five callers in terms of mismatch rate by genotype (Fig. 2A).