Table 1 Number of detected variants across different variant calling tools
Combined analysis | Individual analysisa | ||||
|---|---|---|---|---|---|
SAMtools | UG | SAMtools | UG | HC | |
Nr of SNVs (Ti/Tvb) | Nr of SNVs (Ti/Tvb) | Nr of SNVs (Ti/Tvb) | Nr of SNVs (Ti/Tvb) | Nr of SNVs (Ti/Tvb) | |
Total | 5 165 528 (2.03) | 4 802 404 (1.93) | 3 065 136 (2.12) | 2 650 589 (2.04) | 2 410 162 (2.18) |
Filtered | 4 255 671 (2.19) | 4 471 459 (2.01) | 2 280 929 (2.22) | 2 525 133 (2.09) | 2 363 010 (2.19) |
Knowna | 1 423 628 (2.39) | 1 374 703 (2.40) | 860 320 (2.44) | 896 616 (2.42) | 873 093 (2.44) |
Novel | 2 832 043 (2.10) | 3 096 756 (1.87) | 1 420 609 (2.11) | 1 628 517 (1.94) | 1 489 918 (2.06) |
Nr of INDELs | Nr of INDELs | Nr of INDELs | Nr of INDELs | Nr of INDELs | |
Total | 11 750 679 | 3 539 988 | 3 778 222 | 341 366 | 1 295 497 |
Filtered | 5 635 914 | 2 764 772 | 1 157 392 | 334 763 | 644 610 |
Knownc | 4 188 | 4 129 | 1 493 | 1 001 | 1 422 |
Novel | 5 631 726 | 2 760 643 | 1 155 899 | 333 761 | 643 188 |