Additional file 8.
Table S3 - complete statistics for human genotyping performance comparison. This file contains performance statistics based on the Harsimendy et al.  human data set for Sniper, Maq, and SOAPsnp at different stringency levels for ALL, UNI, and BEST read map types; total SNP loci identified; and putative novel SNPs identified by Sniper. For each program and read map approach, genotypes for four individuals were compared to those determined by ABI Sanger sequencing. The benchmark set (Sanger \ NGS) contains 253 SNPs. True positive rates (TPRs) and false discovery error rates (FDRs) were estimated from these comparisons (top rows). In parentheses, from left to right: matching genotypes; positions identified as SNP but differing in genotype; SNPs not identified by Sanger; Sanger SNPs not identified by program. Sniper SNPs are reported using a stringency threshold on the phred-like posterior probability: Q = -10 log10(1 - P), where Q ≥ 13 (P < 0.05). Maq SNPs were generated using Q ≥ 13 minimum consensus quality, Qadj ≥ 13 minimum adjacent quality, and prior probability of SNP PSNP = 0.001, with default settings otherwise. Soap SNPs were generated using default settings, '-t -u -n', and a 2:1 transition:transversion ratio for prior probability, and PSNP = 0.001. Four SNPs are predicted by Sniper, Maq, and SOAPsnp for k = 2 mismatches, identified by comparison to Sanger benchmark data (Additional file 8). Statistics were generated using Sniper.
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Simola and Kim Genome Biology 2011 12:R55 doi:10.1186/gb-2011-12-6-r55