Sites Called
After applying the additional incremental filtering and reducing each SNP set down to approximately 4x105, 1x105, and 8x104 sites called, HaplotypeCaller, SAMtools, and UnifiedGenotyper were most similar in the specific sites called, sharing at least 44% of sites at each level of filtering (Fig. S3-8). FreeBayes and VarScan called the most sites unique to a single caller; FreeBayes called at least 61% unique sites across these incremental filter levels (Fig. S3-6), and VarScan called 86% unique SNPs in the one comparison it was included in (Fig. S3-4). We found very little difference when comparing the total sites shared between callers (Fig. S3,5,7) and the sites shared with zero genotype mismatches (Fig. 1, S9-10). Notably however, the specific sites each program called that had genotyping mismatches were largely unique to each caller (Fig. 1, S9-10).