Use when you need to identify overlapping genomic regions across multiple BED files simultaneously.
multiIntersectBed -i file1.bed file2.bed [file3.bed ...] [options]/home/vimalinx/miniforge3/envs/bio/bin/multiIntersectBedreferences/help.md-g -empty.# 1) Multi-file overlap segmentation
multiIntersectBed \
-i sample1.bed sample2.bed sample3.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
-names and -header when the output will be read by humans or imported into tables.-empty requires -g.-incl / -excl style constraints do not exist here; this is an overlap partitioning tool, not a shuffler.-h for help; the captured --help path in references is misleading because the wrapper expects other arguments first.