Table 2 Performances (F1 scores in %) of SNP predictions in difficult-to-map regions and Major Histocompatibility Complex (MHC) by NanoCaller, Medaka, Clair, and Longshot on ONT data. These evaluations are performed against v4.2.1 benchmark variants for the Ashkenazim trio (HG002, HG003, and HG004), whereas “HG002 Bonito” and “HG002 R10.3” are different HG002 ONT datasets
Prediction | Variant caller | HG002 | HG003 | HG004 | HG002 Bonito | HG002 R10.3 |
|---|---|---|---|---|---|---|
SNPs on ONT data in difficult-to-map regions | NanoCaller ONT-HG001 | 95.80 | 96.83 | 96.70 | 97.44 | 96.34 |
NanoCaller ONT-HG002 | 96.18 | 96.92 | 96.92 | 97.38 | 96.44 | |
Medaka | 95.41 | 96.46 | 96.46 | 96.51 | 94.20 | |
Clair | 94.98 | 96.27 | 96.12 | 95.63 | 84.83 | |
Longshot | 93.95 | 94.61 | 94.55 | 95.42 | 93.00 | |
SNPs on ONT data in MHC | NanoCaller ONT-HG001 | 98.65 | 99.06 | 99.18 | 99.45 | 98.46 |
NanoCaller ONT-HG002 | 98.86 | 99.19 | 99.28 | 99.46 | 98.69 | |
Medaka | 97.62 | 99.25 | 98.10 | 98.24 | 98.24 | |
Clair | 97.60 | 98.51 | 98.57 | 98.97 | 92.06 | |
Longshot | 68.52 | 73.13 | 69.40 | 68.48 | 68.41 |