Table 3 Comparison of VCMM with other methods using SNP genotyping platforms
From: A practical method to detect SNVs and indels from whole genome and exome sequencing data
| Â | Â | Â | Number | Proportion (%) | ||||
|---|---|---|---|---|---|---|---|---|
| Â | Chip | Â | VCMM | GATK | SAMtools | VCMM | GATK | SAMtools |
WGS | OmniExpress BeadChip | Concordant | 641,860 | 641,538 | 639,112 | 99.816 | 99.766 | 99.389 |
| Â | Â | FN | 1,083 | 1,366 | 3,832 | 0.168 | 0.212 | 0.595 |
| Â | Â | FP | 98 | 137 | 97 | 0.015 | 0.021 | 0.015 |
WES | Exome BeadChip | Concordant | 190,147 | 190,137 | 189,825 | 99.974 | 99.968 | 99.804 |
| Â | Â | FN | 36 | 46 | 361 | 0.019 | 0.024 | 0.190 |
| Â | Â | FP | 14 | 14 | 11 | 0.007 | 0.007 | 0.006 |
