Fig. 1: Number of unique sites shared between FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan after additional filtering to approximately 8x104 sites called. The number of unique sites with zero genotype mismatches (A) and the number of unique sites with at least one genotype mismatch (B) are shown. SNP sets were filtered with depth, genotype quality, and quality score where applicable. FreeBayes, HaplotypeCaller, SAMtools, UnifiedGenotyper, and VarScan resulted in 79,970, 79,931, 77,928, 79,990, 79,650 sites respectively.