Table 3 Performance of Clairvoyante on PacBio data at common variant sites in 1KGp3
From: A multi-task convolutional deep neural network for variant calling in single molecule sequencing
Seq. tech. | Model trained on | Trained epochs | Ending learning rate and lambda | Call variants in | Best variant quality cutoff | Overall FPR (%) | Overall FNR (%) | Overall precision (%) | Overall F1 score (%) | SNP FPR (%) | SNP FNR (%) | SNP precision (%) | SNP F1 score (%) | Indel FPR (%) | Indel FNR (%) | Indel precision (%) | Indel F1 score (%) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PacBio | HG001 | 50a | 1.E−05 | HG001 | 69 | 1.51 | 7.41 | 98.38 | 95.39 | 0.32 | 1.43 | 99.68 | 99.12 | 10.94 | 60.59 | 76.24 | 51.96 |
999 | 1.E−03 | 94 | 1.39 | 7.07 | 98.51 | 95.64 | 0.26 | 1.29 | 99.74 | 99.22 | 10.39 | 58.41 | 78.21 | 54.31 | |||
1499 | 1.E−04 | 89 | 2.17 | 6.06 | 97.70 | 95.78 | 0.25 | 1.18 | 99.75 | 99.28 | 16.44 | 49.38 | 72.02 | 59.45 | |||
1999 | 1.E−05 | 85 | 2.43 | 5.81 | 97.43 | 95.78 | 0.26 | 1.18 | 99.74 | 99.28 | 18.20 | 46.98 | 70.44 | 60.50 | |||
HG001 | 50a | 1.E−05 | HG002 | 75 | 1.78 | 7.48 | 98.07 | 95.22 | 0.71 | 1.47 | 99.28 | 98.91 | 10.29 | 60.05 | 77.70 | 52.77 | |
999 | 1.E−03 | 96 | 1.98 | 7.31 | 97.87 | 95.21 | 0.75 | 1.45 | 99.23 | 98.89 | 11.54 | 58.54 | 76.08 | 53.67 | |||
1499 | 1.E−04 | 114 | 2.07 | 7.77 | 97.76 | 94.91 | 0.76 | 1.45 | 99.23 | 98.89 | 12.21 | 63.04 | 72.67 | 49.00 | |||
1999 | 1.E−05 | 123 | 1.97 | 7.94 | 97.86 | 94.87 | 0.75 | 1.44 | 99.24 | 98.90 | 11.50 | 64.74 | 73.09 | 47.57 | |||
HG002 | 72a | 1.E−05 | HG001 | 56 | 1.63 | 9.22 | 98.20 | 94.35 | 0.49 | 2.55 | 99.49 | 98.46 | 10.72 | 68.46 | 72.43 | 43.94 | |
999 | 1.E−03 | 99 | 1.69 | 8.47 | 98.16 | 94.73 | 0.57 | 1.84 | 99.42 | 98.79 | 10.62 | 67.39 | 73.31 | 45.14 | |||
1499 | 1.E−04 | 116 | 2.43 | 8.25 | 97.36 | 94.47 | 0.80 | 1.91 | 99.19 | 98.64 | 14.89 | 64.53 | 66.97 | 46.37 | |||
1999 | 1.E−05 | 127 | 2.34 | 8.57 | 97.45 | 94.34 | 0.89 | 2.04 | 99.09 | 98.52 | 13.56 | 66.58 | 68.06 | 44.83 | |||
HG002 | 72a | 1.E−05 | HG002 | 55 | 1.88 | 7.08 | 97.98 | 95.38 | 0.55 | 1.25 | 99.44 | 99.10 | 12.15 | 58.10 | 75.20 | 53.82 | |
999 | 1.E−03 | 88 | 1.86 | 6.59 | 98.01 | 95.66 | 0.49 | 1.15 | 99.51 | 99.18 | 12.45 | 54.11 | 76.34 | 57.32 | |||
1499 | 1.E−04 | 101 | 2.02 | 5.81 | 97.85 | 95.99 | 0.42 | 1.02 | 99.57 | 99.28 | 14.10 | 47.73 | 76.11 | 61.98 | |||
1999 | 1.E−05 | 101 | 2.05 | 5.70 | 97.83 | 96.03 | 0.41 | 0.99 | 99.59 | 99.30 | 14.40 | 46.87 | 75.96 | 62.52 | |||
GATK UnifiedGenotyper, HG001 | 1 | 0.83 | 99.92 | 8.19 | 0.15 | 0.94 | 99.91 | 8.19 | 0.17 | – | – | – | – | ||||
GATK HaplotypeCaller, HG001 | 1 | 0.08 | 97.91 | 52.26 | 4.02 | 0.06 | 97.65 | 61.16 | 4.53 | 0.67 | 99.98 | 0.39 | 0.04 | ||||
GATK UnifiedGenotyper, HG002 | 1 | 0.75 | 99.91 | 9.91 | 0.17 | 0.85 | 99.90 | 9.91 | 0.19 | – | – | – | – | ||||
GATK HaplotypeCaller, HG002 | 1 | 0.69 | 98.74 | 63.81 | 2.47 | 0.79 | 98.58 | 63.88 | 2.78 | 0.02 | 100.00 | 15.66 | 0.007 | ||||
