Comparing variant caller programs
Variant callers differed considerably in the number of sites they called using the baseline filtering (e.g., UnifiedGenotyper yielded ~3M vs. ~80k for VarScan; Table 2). We found that the mismatch rates between parent and offspring genotype calls roughly scaled with the number of SNPs called (Table 2; Fig. S1), and in order to compare mismatch rates between different callers we standardized their output by adjusting the filtering criteria so that each caller yielded a similar number of SNPs (Table S1-5). This additional filtering step was conducted in an iterative manner to assess the effect of varying stringency on mismatch rates, using the QUAL, DP, and GQ metrics (but only DP and GQ for VarScan) and varying each metric according to their empirical distribution. For example, to get approximately x SNPs with a given caller, we would increase the QUAL, DP, and GP filtering criteria from they th to the z thpercentile of each of their respective distributions. We calculated two different mismatch rates, a by-genotype rate and a by-site rate, defined respectively as the number of mismatched parent-offspring genotype calls out of the total number of genotypes called and the number of sites with at least one mismatched parent-offspring genotype call out of the total number of sites.