From: Ratatosk: hybrid error correction of long reads enables accurate variant calling and assembly
SNPs | Indels | ||||||
---|---|---|---|---|---|---|---|
Precision | Recall | F1 | Precision | Recall | F1 | ||
(a) Variants with quality scores below a threshold automatically computed by rtg-tools are filtered out | |||||||
HG002 | Raw | 98.87 | 97.93 | 98.25 | 81.83 | 39.26 | 53.06 |
FMLRC | 96.42 | 96.31 | 96.37 | 89.96 | 80.55 | 85.00 | |
Ratatosk | 97.84 | 99.10 | 98.47 | 92.10 | 89.19 | 90.62 | |
HG003 | Raw | 99.16 | 98.85 | 99.00 | 84.00 | 47.62 | 60.78 |
FMLRC | 97.73 | 97.56 | 97.64 | 92.78 | 85.38 | 88.93 | |
Ratatosk | 98.94 | 99.42 | 99.18 | 94.04 | 92.14 | 93.08 | |
HG004 | Raw | 99.19 | 98.73 | 98.96 | 83.67 | 45.50 | 58.94 |
FMLRC | 97.22 | 97.44 | 97.33 | 90.11 | 84.52 | 87.23 | |
Ratatosk | 98.56 | 99.46 | 99.01 | 92.65 | 91.38 | 92.01 | |
(b) All variants with the FILTERfield set to PASS in the VCF files are used | |||||||
HG002 | Raw | 85.32 | 99.69 | 91.94 | 11.60 | 72.96 | 20.02 |
FMLRC | 78.08 | 99.57 | 87.52 | 60.20 | 93.47 | 73.23 | |
Ratatosk | 90.22 | 99.82 | 94.78 | 86.07 | 96.09 | 90.80 | |
HG003 | Raw | 95.15 | 99.74 | 97.39 | 15.44 | 77.19 | 25.73 |
FMLRC | 86.73 | 99.58 | 92.72 | 69.99 | 93.26 | 79.97 | |
Ratatosk | 95.94 | 99.80 | 97.83 | 88.38 | 95.83 | 91.95 | |
HG004 | Raw | 93.34 | 99.80 | 96.47 | 14.83 | 75.98 | 24.81 |
FMLRC | 84.08 | 99.68 | 91.21 | 66.87 | 94.60 | 78.35 | |
Ratatosk | 93.05 | 99.87 | 96.34 | 87.77 | 96.69 | 92.02 |