1. 1. Quick Start guides
   1. 1.1. Constructing bedMethyl tables
      1. 1.1.1. Migrating to v0.6.0
   2. 1.2. Make hemi-methylation bedMethyl tables
   3. 1.3. Updating and adjusting MM tags
   4. 1.4. Inspecting base modification probabilities
   5. 1.5. Summarizing a modBAM
   6. 1.6. Calculating modification statistics in regions
   7. 1.7. Calling mods in a modBAM
   8. 1.8. Removing modification calls at the ends of reads
   9. 1.9. Repair MM/ML tags on trimmed reads
   10. 1.10. Working with sequence motifs
       1. 1.10.1. Making a motif BED file
       2. 1.10.2. Find highly modified motif sequences
       3. 1.10.3. Evaluate and refine a table of known motifs
       4. 1.10.4. Structured logging schema
   11. 1.11. Extracting read information to a table
   12. 1.12. Investigating patterns with localise
   13. 1.13. Perform differential methylation scoring
   14. 1.14. Validate ground truth results
   15. 1.15. Calculating methylation entropy
   16. 1.16. Narrow output to specific positions
   17. 1.17. Manipulate bedMethyl files
   18. 1.18. Check modified base tags
   19. 1.19. Find regions of accessible chromatin
2. 2. Extended subcommand help
3. 3. Troubleshooting
4. 4. Frequently asked questions
5. 5. Current limitations
6. 6. Performance considerations
7. 7. Algorithm details
   1. 7.1. Pass/fail base modification calls
      1. 7.1.1. Threshold examples
      2. 7.1.2. Numeric details
   2. 7.2. DMR model and scoring details
   3. 7.3. Ignoring and combining calls