5. The BEDTools suite¶
bedtools consists of a suite of sub-commands that are invoked as follows:
bedtools [sub-command] [options]
For example, to intersect two BED files, one would invoke the following:
bedtools intersect -a a.bed -b b.bed
5.1. The full list of bedtools sub-commands.¶
- 5.1.1. annotate
- 5.1.2. bamtobed
- 5.1.3. bamtofastq
- 5.1.4. bed12tobed6
- 5.1.5. bedpetobam
- 5.1.6. bedtobam
- 5.1.7. closest
- 5.1.8. cluster
- 5.1.9. complement
- 5.1.10. coverage
- 5.1.11. expand
- 5.1.12. flank
- 5.1.13. genomecov
- 5.1.14. getfasta
- 5.1.15. groupby
- 5.1.16. igv
- 5.1.17. intersect
- 5.1.18. jaccard
- 5.1.19. links
- 5.1.20. makewindows
- 5.1.21. map
- 5.1.22. maskfasta
- 5.1.23. merge
- 5.1.24. multicov
- 5.1.25. multiinter
- 5.1.26. nuc
- 5.1.27. overlap
- 5.1.28. pairtobed
- 5.1.29. pairtopair
- 5.1.30. random
- 5.1.31. reldist
- 5.1.32. shuffle
- 5.1.33. slop
- 5.1.34. sort
- 5.1.35. subtract
- 5.1.36. tag
- 5.1.37. unionbedg
- 5.1.38. window
