From: Comparing a few SNP calling algorithms using low-coverage sequencing 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 |