Research Article
A Comparison of Variant Calling Pipelines Using Genome in a Bottle as a Reference
Table 5
Average Positive Predictive Value (PPV) and sensitivity for each tool.
| | Tool | Average SNV PPV | Average SNV sensitivity | Average indel PPV | Average indel sensitivity |
| | Bowtie2 | 98.69% | 49.19% | 45.45% | 32.69% | | BWA mem | 99.15% | 50.96% | 43.24% | 33.10% | | BWA sampe | 99.09% | 50.85% | 45.31% | 31.30% | | CUSHAW3 | 80.69% | 48.08% | 29.50% | 29.74% | | MOSAIK | 98.51% | 35.79% | 52.95% | 28.63% | | Novoalign | 99.17% | 50.18% | 44.55% | 31.70% | | FreeBayes | 90.95% | 51.00% | 35.86% | 32.79% | | GATK HaplotypeCaller | 97.05% | 51.03% | 43.17% | 31.79% | | GATK UnifiedGenotyper | 97.93% | 50.77% | 52.12% | 31.57% | | SAMtools mpileup | 94.99% | 50.76% | 39.15% | 31.30% | | SNPSVM | 99.92% | 50.85% | N/A | N/A |
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