Table 2 Effects of submitting multiple and individual pooled BAM files to each program
From: Evaluation of variant detection software for pooled next-generation sequence data
a | ||||
|---|---|---|---|---|
Group Size | Sen% | FP% | BA% | SD% |
CRISP-2 pools | 97.8 | 10.5 | 93.7 | 95.3 |
CRISP-4 pools | 96.1 | 7.5 | 94.3 | 91.6 |
CRISP-8 pools | 97.2 | 7.4 | 94.9 | 94.1 |
SNVer-1 pool | 72.4 | 3.3 | 84.6 | 52.9 |
SNVer-2 pools | 71.4 | 3.3 | 84.1 | 51 |
SNVer-4 pools | 70.4 | 3.3 | 83.6 | 49 |
SNVer-8 pools | 69.4 | 3.2 | 83.1 | 47.1 |
VarScan-1 pool | 29.3 | 0.1 | 64.6 | 0.1 |
VarScan-2 pools | 29.3 | 0.1 | 64.6 | 0.1 |
VarScan-4 pools | 29.3 | 0.1 | 64.6 | 0.1 |
VarScan-8 pools | 29.2 | 0.1 | 64.5 | 0.1 |
GATK-1 pool | 98.2 | 9.1 | 94.6 | 95.9 |
GATK-2 pools | 98.2 | 9 | 94.6 | 95.8 |
GATK-4 pools | 98.1 | 8.6 | 94.7 | 95.5 |
GATK-8 pools | 98 | 8.5 | 94.7 | 95.1 |
b | ||||
Group Size | Sen% | FP% | BA% | SD% |
CRISP-2 pools | 97.1 | 4.1 | 96.5 | 93.2 |
CRISP-4 pools | 92.2 | 4 | 94.1 | 83.4 |
SNVer-1 pool | 74.4 | 1 | 86.7 | 53.6 |
SNVer-2 pools | 73.7 | 1 | 86.3 | 52.5 |
SNVer-4 pools | 72.8 | 1 | 85.9 | 50.8 |
VarScan-1 pool | 41 | 0 | 70.5 | 3.1 |
VarScan-2 pools | 41 | 0 | 70.5 | 3.1 |
VarScan-4 pools | 40.9 | 0 | 70.5 | 3.1 |
GATK-1 pool | 98 | 0.2 | 98.9 | 95.2 |
GATK-2 pools | 97.9 | 0.2 | 98.9 | 95.1 |
GATK-4 pools | 97.9 | 0.2 | 98.9 | 95 |