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Table 1 Variant calling performance on sequencing datasets P1-P4 generated for four ovarian cancer patients

From: Semi-supervised learning for somatic variant calling and peptide identification in personalized cancer immunotherapy

DataSet Caller # calls TP FP TN FN TPR PPV F1
P1 SNVQ 515 48 114 0 0 100 29.63 45.71
P: 65 Strelka 435 48 34 80 0 100 58.54 73.85
U: 29758 2CP 65 41 8 106 7 85.42 83.67 84.54
Reseq: 162 PLATO 587 42 6 104 10 80.77 87.5 84
P2 SNVQ 597 147 65 3 2 98.66 69.34 81.44
P: 187 Strelka 619 149 59 9 0 100 71.63 83.47
U: 31210 2CP 187 133 39 29 16 89.26 77.33 82.87
Reseq: 217 PLATO 449 144 43 25 5 96.64 77.01 85.71
P3 SNVQ 629 61 13 8 1 98.39 82.43 89.71
P: 76 Strelka 306 62 11 10 0 100 84.93 91.85
U: 30289 2CP 76 57 1 20 5 91.94 98.28 95
Reseq: 83 PLATO 429 62 3 18 0 100 95.38 97.64
P4 SNVQ 482 48 23 87 2 96 67.61 79.34
P: 67 Strelka 380 50 94 16 0 100 34.72 51.55
U: 30176 2CP 67 45 2 108 5 90 95.74 92.78
Reseq: 160 PLATO 490 48 7 103 2 96 87.27 91.43