What it does

This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files. The pictorial and raw data examples below illustrate the behavior of this tool more clearly.

This tool requires that each BED file is reference-sorted (chrom, then start).

This tool requires that bedtools has been installed on your system.

The output file will contain five fixed columns, plus additional columns for each BED file:

• 1. Chromosome name (or 'genome' for whole-genome coverage).
• 2. The zero-based start position of the interval.
• 3. The one-based end position of the interval.
• 4. The number of input files that had at least one feature overlapping this interval.
• 5. A list of input files or labels that had at least one feature overlapping this interval.
• 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval.

Example input:

# a.bed
chr1  6   12
chr1  10  20
chr1  22  27
chr1  24  30

# b.bed
chr1  12  32
chr1  14  30

# c.bed
chr1  8   15
chr1  10  14
chr1  32  34

Example without a header and without reporting intervals with zero coverage:

chr1        6       8       1       1       1       0       0
chr1        8       12      2       1,3     1       0       1
chr1        12      15      3       1,2,3   1       1       1
chr1        15      20      2       1,2     1       1       0
chr1        20      22      1       2       0       1       0
chr1        22      30      2       1,2     1       1       0
chr1        30      32      1       2       0       1       0
chr1        32      34      1       3       0       0       1

Example adding a header line:

chrom       start   end     num     list    a.bed   b.bed   c.bed
chr1        6       8       1       1       1       0       0
chr1        8       12      2       1,3     1       0       1
chr1        12      15      3       1,2,3   1       1       1
chr1        15      20      2       1,2     1       1       0
chr1        20      22      1       2       0       1       0
chr1        22      30      2       1,2     1       1       0
chr1        30      32      1       2       0       1       0
chr1        32      34      1       3       0       0       1

Example adding a header line and custom file labels:

chrom       start   end     num     list        joe bob     sue
chr1        6       8       1       joe         1   0       0
chr1        8       12      2       joe,sue     1   0       1
chr1        12      15      3       joe,bob,sue 1   1       1
chr1        15      20      2       joe,bob     1   1       0
chr1        20      22      1       bob         0   1       0
chr1        22      30      2       joe,bob     1   1       0
chr1        30      32      1       bob         0   1       0
chr1        32      34      1       sue         0   0       1

This tool is part of the bedtools package from the Quinlan laboratory. If you use this tool, please cite Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.