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).