Data sets | CASAVA | GATK | Common | |||||
---|---|---|---|---|---|---|---|---|
 | Variant count | TsTv ratio | Variant count | TsTv ratio | Variant count | TsTv ratio | ||
Omni Array Genotyping Data | Â | Â | Â | Â | Â | Â | ||
108 unrelated (per sample) | All | SNP by pipelines | 708,089 ± 4,516 | 3.56 ± 0.003 | 715,033 ± 4,551 | 3.53 ± 0.003 | 706,378 ± 4502 | 3.57 ± 0.003 |
GT Matched SNP | 705,749 ± 4468 | 3.58 ± 0.003 | 703,608 ± 4479 | 3.59 ± 0.003 | 698,910 ± 4437 | 3.60 ± 0.003 | ||
Ref or missing by pipeline | 1661347 ± 4538 |  | 1654613 ± 4573 |  | 1649566 ± 4567 |  | ||
False positive | 988 ± 20 | 1.46 ± 0.020 | 6320 ± 112 | 1.61 ± 0.039 | 489 ± 13 | 1.92 ± 0.031 | ||
False negative | 23283 ± 90 |  | 22076 ± 58 |  | 20550 ± 59 |  | ||
PASS | SNP by pipelines | 707,128 ± 4506 | 3.57 ± 0.003 | 696,960 ± 4480 | 3.60 ± 0.003 | 695,589 ± 4456 | 3.60 ± 0.003 | |
GT Matched SNP | 705,106 ± 4459 | 3.58 ± 0.003 | 693,135 ± 4434 | 3.63 ± 0.003 | 689,330 ± 4394 | 3.63 ± 0.003 | ||
Ref or missing by pipeline | 1662325 ± 4528 |  | 1672894 ± 4501 |  | 1657868 ± 4533 |  | ||
False positive | 810 ± 17 | 1.33 ± 0.019 | 277 ± 20 | 2.23 ± 0.054 | 229 ± 10 | 2.12 ± 0.054 | ||
False negative | 24067 ± 134 |  | 33985 ± 96 |  | 22735 ± 65 |  | ||
NGS Data Set | Â | Â | Â | Â | Â | Â | ||
108 unrelated (per sample) | All | 4,025,625 ± 44,102 | 2.02 ± 0.001 | 4,331,336 ± 45,896 | 1.86 ± 0.002 | 3,792,293 ± 43,122 | 2.07 ± 0.000 | |
PASS | 3,894,810 ± 43,388 | 2.04 ± 0.001 | 3,438,203 ± 41205 | 2.13 ± 0.001 | 3,401,091 ± 40317 | 2.15 ± 0.001 | ||
19 trios ( per trio) | ALL | 5,235,184 ± 47,790 | 2.01 ± 0.001 | 7,003,439 ± 56,488 | 1.88 ± 0.003 | 4,945,042 ± 46,650 | 2.06 ± 0.002 | |
PASS | 4,786,871 ± 47,564 | 2.07 ± 0.002 | 5,125,002 ± 48,717 | 2.13 ± 0.001 | 4,320,414 ± 43,062 | 2.14 ± 0.001 | ||
Family 1 | ALL | 6,082,624 | 2.00 | 6,337,108 | 1.88 | 5,635,183 | 2.04 | |
PASS | 5,438,393 | 2.07 | 5,004,048 | 2.12 | 4,898,126 | 2.13 | ||
Family 2 | ALL | 5,192,891 | 1.99 | 5,459,725 | 1.84 | 4,752,193 | 2.03 | |
PASS | 4,526,291 | 2.07 | 4,205,995 | 2.12 | 4,104,343 | 2.13 |