Table 11 Number of SNVs called by each of the four algorithms with different coverage cutoffs
From: Comparing a few SNP calling algorithms using low-coverage sequencing data
Coverage cutoffs | SOAPsnp | Atlas-SNP2 | GATK-UGT | SAMtools |
|---|---|---|---|---|
≥ 3X | 877 (537, 340) | 539 (393, 146) | 650 (427, 223) | 570 (398, 172) |
≥ 4X | 397 (230, 167) | 291 (195, 96) | 309 (187, 122) | 270 (174, 96) |
≥ 5X | 280 (162, 118 ) | 218 (138, 80) | 223 (127, 96) | 203 (121, 82) |
≥ 6X | 222 (130, 92) | 187 (116, 71) | 186 (105, 81) | 167 (100, 67) |
≥ 7X | 194 (115, 79) | 160 (99, 61) | 156 (93, 63) | 145 (87, 58) |
≥ 8X | 168 (99, 69) | 145 (93, 52) | 134 (81, 53) | 127 (81, 46) |
≥ 9X | 153 (88, 65) | 138 (87, 51) | 126 (75, 51) | 115 (73, 42) |
≥ 10X | 137 (78, 59) | 126 (82, 44) | 111 (65, 46) | 100 (64, 36) |