Table 1 Number of called mutations (number of SNVs and indels given in brackets) and artefacts, sensitivity (sens), positive predictive value (PPV) and the F1 score regarding the eight variant calling tools investigated in case of the first and second dataset.
From: Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data
Variant caller | First real dataset (HiSeq) | Second real dataset (NextSeq) | ||||||||
|---|---|---|---|---|---|---|---|---|---|---|
Mutations (SNVs + indels) | Artefacts | Sens | PPV | F1 score | Mutations (SNVs + indels) | Artefacts | Sens | PPV | F1 score | |
GATK | 94 (76 + 18) | 55 | 0.83 | 0.63 | 0.72 | 156 (112 + 44) | 209 | 0.69 | 0.43 | 0.53 |
Platypus | 95 (76 + 19) | 67 | 0.84 | 0.58 | 0.69 | 189 (136 + 53) | 791 | 0.83 | 0.19 | 0.31 |
VarScan | 85 (69 + 15) | 7 | 0.75 | 0.92 | 0.83 | 91 (84 + 7) | 109 | 0.40 | 0.46 | 0.43 |
LoFreq | 111 (91 + 20) | 503 | 0.98 | 0.18 | 0.31 | 178 (121 + 57) | 1,650 | 0.79 | 0.10 | 0.17 |
FreeBayes | 113 (93 + 20) | 7,918 | 1.00 | 0.01 | 0.03 | 178 (162 + 16) | 35,126 | 0.79 | 0.01 | 0.01 |
SNVer | 94 (76 + 18) | 24 | 0.83 | 0.80 | 0.81 | 127 (72 + 55) | 4,389 | 0.56 | 0.03 | 0.05 |
SAMtools | 72 (70 + 2) | 37 | 0.64 | 0.65 | 0.65 | 73 (71 + 2) | 111 | 0.32 | 0.40 | 0.36 |
VarDict | 109 (90 + 19) | 9 | 0.96 | 0.92 | 0.94 | 205 (155 + 50) | 3,517 | 0.91 | 0.06 | 0.10 |
Ground truth | 113 (93 + 20) | 0 | 226 (168 + 58) | 0 | ||||||
