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.