cheatsheet.txt

# merge
bedtools merge -i ifile.bed -c 4 -o collapse # print the merged feature names (4th column)

# intersect
$ cat A.bed
chr1  10  20
chr1  30   40

$ cat B.bed
chr1  15  20

$ bedtools intersect -a A.bed -b B.bed -wa # print only intersecting entry in A.bed
chr1  10   20

$ bedtools intersect -a A.bed -b B.bed -wa -wb # print both intersecting entries in A.bed and B.bed
chr1  10  20  chr1 15  20