# Basic syntax: sort -V -k1,1 -k2,2 input_file.bed > sorted_file.bed # This sorts alphanumerically by chromosome and then byvstart position # and then by end position, producing a file order like: chr1 1 10 chr1 2 5 chr2 1 10 . . . . . . . . . chr10 1 10 . . . . . . . . . chrX 1 10 chrY 1 10