Table 5

Number of SNVs called by each of the four algorithms using raw and trimmed data
A. In raw data
≥ 3X* dbSNPs Non-dbSNPs
SOAPsnp 940 545 395
Atlas-SNP2 432 315 117
SAMtools 532 376 156
GATK-UGT 669 444 225
B. In trimmed data
≥ 3X* dbSNPs Non-dbSNPs
SOAPsnp 968 564 404
Atlas-SNP2 448 321 127
SAMtools 570 398 172
GATK-UGT 729 478 251

* Atlas-SNP2 requires at least 3X to call a SNV. For the other three algorithms, we choose the called SNVs with ≥ 3X coverage.

Yu and Sun

Yu and Sun BMC Bioinformatics 2013 14:274   doi:10.1186/1471-2105-14-274

Open Data