Table 2 Online comparison of Bystro and recent programs in filtering 8.49 × 107 variants from 1000 Genomes
From: Bystro: rapid online variant annotation and natural-language filtering at whole-genome scale
Group | Search query | Time (s) | Variants | Tr:Tv |
|---|---|---|---|---|
1 | Exonic | 0.030 ± 0.030 | 993,343 | 2.96 |
2 (a) | cadd > 20 maf < .001 pathogenic expert review missense | 0.029 ± 0.009 | 65 | 1.71 |
2 (b) | cadd > 20 maf < .001 pathogenic expert’s review non-synonymous | 0.036 ± 0.019 | 65 | 1.71 |
2 (c) | cadd > 20 maf < .001 pathogen expert-reviewed nonsynonymous | 0.044 ± 0.025 | 65 | 1.71 |
3 (a) | Early onset breast cancer | 0.046 ± 0.029 | 4335 | 2.51 |
3 (b) | Early-onset breast cancer | 0.037 ± 0.020 | 4335 | 2.51 |
3 (c) | Early onset breast cancers | 0.033 ± 0.015 | 4335 | 2.51 |
4 (a) | Pathogenic nonsense Ehlers-Danlos | 0.038 ± 0.027 | 1 | NA |
4 (b) | Pathogenic nonsense E.D.S | 0.078 ± 0.087 | 1 | NA |
4 (c) | Pathogenic stopgain eds | 0.040 ± 0.022 | 1 | NA |