From: Measuring, visualizing, and diagnosing reference bias with biastools
Bowtie 2 | BWA-MEM | BWA-MEM (-L 30) | Minimap2 | Giraffe-linear | Giraffe-major | Giraffe-pop5 | Giraffe-1KGP | ||
---|---|---|---|---|---|---|---|---|---|
SNV | Balanced | 52,173 | 52,133 | 52,336 | 52,148 | 52,267 | 52,267 | 52,353 | 52,402 |
Bias (loss) | 2108 | 2084 | 1881 | 2028 | 1924 | 1911 | 1812 | 1752 | |
Bias (flux) | 495 | 569 | 594 | 581 | 566 | 561 | 548 | 573 | |
Bias (local) | 169 | 177 | 158 | 186 | 183 | 210 | 228 | 211 | |
Outliers | 78 | 60 | 54 | 80 | 83 | 74 | 82 | 85 | |
Gap | Balanced | 10,386 | 10,143 | 10,519 | 10,213 | 10,308 | 10,323 | 10,336 | 10,358 |
Bias (loss) | 628 | 799 | 435 | 726 | 659 | 630 | 600 | 571 | |
Bias (flux) | 112 | 146 | 150 | 160 | 137 | 143 | 139 | 142 | |
Bias (local) | 122 | 165 | 149 | 161 | 151 | 156 | 177 | 180 | |
Outliers | 22 | 17 | 17 | 10 | 15 | 18 | 18 | 19 |