Reference Code backup Executable files
Compute the amount of overlap or distance between feature coordinates occurring on the same input line and reports the result at the end of the same line.
bedtools overlap -i <in.bed|stdin> -cols <str>
This tool is part of the bedtools suite, and it's also known as getOverlap.
The overlap tool from bedtools computes the amount of overlap (in the case of positive values) or distance (in the case of negative values) between feature coordinates occurring on the same input line and reports the result at the end of the same line.
-i str: Input file. Use stdin for pipes.
-cols str: Specify the columns (1-based) for the starts and ends of the features for which you'd like to compute the overlap/distance. The columns must be listed in the following order: start1,end1,start2,end2.
Examples
Assume you have two sets of genomic features and you want to calculate how many base pairs they overlap or how far they are away from each other. In this case, you can use getOverlap to get the numbers.
The input file looks like:
$ head input.bed chr1 10 20 A chr1 15 25 B chr1 10 20 C chr1 25 35 D
Now let's do the calculation:
$ bedtools overlap -i input.bed -cols 2,3,6,7 chr1 10 20 A chr1 15 25 B 5 # overlap between A and B chr1 10 20 C chr1 25 35 D -5 # distance between C and D
# you will get the same results if you run getOverlap
$ getOverlap -i input.bed -cols 2,3,6,7 chr1 10 20 A chr1 15 25 B 5 chr1 10 20 C chr1 25 35 D -5