Multi Intersect Bed

# 2) Add a header with readable file names
multiIntersectBed \
  -header \
  -names tumor normal blacklist \
  -i tumor.bed normal.bed blacklist.bed

# 3) Include empty regions across the genome
multiIntersectBed \
  -i a.bed b.bed \
  -g genome.txt \
  -empty

Recommended Workflow

1. Sort every input file by chromosome and start before running the tool.
2. Decide whether you need just overlapping segmentation or also empty regions from a genome definition.
3. Use -names and -header when the output will be read by humans or imported into tables.
4. Post-process the membership columns to define how many files must support a region for your biological question.

Guardrails

• Each interval file must be sorted by chromosome and start.
• This tool segments coordinate space; the output intervals are often smaller than the original input intervals.
• -empty requires -g.
• -incl / -excl style constraints do not exist here; this is an overlap partitioning tool, not a shuffler.
• Prefer -h for help; the captured --help path in references is misleading because the wrapper expects other arguments first.