Table 2 Percent of SNP and INDEL calling sensitivity in NA12878
From: An analytical workflow for accurate variant discovery in highly divergent regions
Mapper | Caller | SNP | INDEL | |||
|---|---|---|---|---|---|---|
| Â | Â | Non-HLA | HLA | HLA-DRB1 | Non-HLA | HLA |
BWA | FreeBayes | 95.8 | 76.0 | 49.3 | 72.9 | 50.0 |
BWA | GATK HC | 94.9 | 76.9 | 58.0 | 83.3 | 61.3 |
BWA | GATK UG | 96.0 | 80.5 | 78.3 | 74.4 | 46.7 |
BWA | Platypus | 94.0 | 71.9 | 50.7 | 86.1 | 60.0 |
BWA | SAMtools | 95.7 | 75.3 | 58.2 | 51.7 | 48.4 |
GSNAP | FreeBayes | 95.6 | 80.3 | 59.4 | 75.2 | 46.7 |
GSNAP | GATK HC | 96.1 | 90.0 | 72.5 | 85.7 | 77.4 |
GSNAP | GATK UG | 97.0 | 91.7 | 100.0 | 76.3 | 51.6 |
GSNAP | Platypus | 95.2 | 77.8 | 42.6 | 87.7 | 70.0 |
GSNAP | SAMtools | 96.3 | 88.3 | 87.9 | 55.6 | 51.6 |
NextGenMap | FreeBayes | 95.5 | 79.2 | 48.5 | 68.6 | 46.7 |
NextGenMap | GATK HC | 94.1 | 79.0 | 62.3 | 81.5 | 67.7 |
NextGenMap | GATK UG | 94.5 | 83.2 | 76.5 | 66.9 | 41.9 |
NextGenMap | Platypus | 92.8 | 72.8 | 38.2 | 76.5 | 50.0 |
NextGenMap | SAMtools | 94.8 | 78.6 | 60.6 | 47.1 | 32.3 |
Novoalign | FreeBayes | 94.9 | 80.1 | 59.4 | 76.1 | 50.0 |
Novoalign | GATK HC | 95.4 | 89.3 | 75.4 | 84.0 | 67.7 |
Novoalign | GATK UG | 95.6 | 89.7 | 85.5 | 78.2 | 54.8 |
Novoalign | Platypus | 93.8 | 79.3 | 53.6 | 88.6 | 73.3 |
Novoalign | SAMtools | 94.7 | 87.4 | 83.8 | 60.2 | 54.8 |
Stampy | FreeBayes | 96.0 | 82.7 | 65.2 | 81.4 | 53.3 |
Stampy | GATK HC | 94.9 | 87.1 | 72.5 | 86.4 | 83.9 |
Stampy | GATK UG | 95.4 | 87.4 | 82.6 | 63.9 | 51.6 |
Stampy | Platypus | 93.5 | 78.8 | 53.7 | 91.2 | 73.3 |
Stampy | SAMtools | 95.1 | 86.6 | 79.4 | 68.5 | 51.7 |