TABLE 1.
Number of true positive SNPs (low‐high), number of false positive SNPs (low‐high), potential for (bisulphite‐induced) ascertainment bias (low‐high), and additional requirements for SNP calling for the seven tools tested
| Tool name (strategy) | Number of true positive SNP | Number of false positive SNP | Potential for ascertainment bias | Requirement |
|---|---|---|---|---|
| bis‐snp (BQ score recalibration) | Low | Low | Medium | List of known SNPs |
| bis‐snp (no BQ score recalibration) | Low | Low | High | |
| biscuit | High | High | High | |
| bs‐snper | Medium | Medium | High | |
| cgmaptools (Bayesian strategy) | Medium | Low | Medium | |
| cgmaptools (binomial strategy) | Medium | Medium | Medium | |
| epidiverse | Medium | Medium | High | |
| methylextract | Medium | Medium | High | |
| gembs | Medium | Medium | High |
Abbreviation: BQ, base quality.