---
name: "bedops"
section: "1"
platform: "linux"
package: "bedops"
version: "2.4.41+dfsg-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/bedops"
---

# bedops(1)

manual page for bedops 2.4.41+dfsg

## NAME

bedops - manual page for bedops 2.4.41+dfsg

## DESCRIPTION

bedops

-

  citation: http://bioinformatics.oxfordjournals.org/content/28/14/1919.abstract

-

  https://doi.org/10.1093/bioinformatics/bts277

- version:

  2\.4.41 (typical)

- authors:

  Shane Neph & Scott Kuehn

-

  USAGE: bedops \[process-flags\] \<operation\> \<File(s)\>\*

-

  Every input file must be sorted per the sort-bed utility. Each operation requires a minimum number of files as shown below.

-

  There is no fixed maximum number of files that may be used.

-

  Input files must have at least the first 3 columns of the BED specification. The program accepts BED and Starch file formats. May use '-' for a file to indicate reading from standard input (BED format only).

-

  Process Flags:

**--chrom** \<chromosome\> Jump to and process data for given \<chromosome\> only.

- **--ec**

  Error check input files (slower).

- **--header**

  Accept headers (VCF, GFF, SAM, BED, WIG) in any input file.

- **--help**

  Print this message and exit successfully.

- **--help-**\<operation\>

  Detailed help on \<operation\>. An example is **--help-c** or **--help-complement**

- **--range** L:R

  Add 'L' bp to all start coordinates and 'R' bp to end coordinates. Either value may be + or - to grow or shrink regions.  With the **-e**/-n operations, the first (reference) file is not padded, unlike all other files.

- **--range** S

  Pad or shrink input file(s) coordinates symmetrically by S. This is shorthand for: **--range** **-S**:S.

- **--version**

  Print program information.

-

  Operations: (choose one of)

**-c**, **--complement** \[-L\] File1 \[File\]\*

**-d**, **--difference** ReferenceFile File2 \[File\]\*

**-e**, **--element-of** \[bp \| percentage\] ReferenceFile File2 \[File\]\*

- by default, **-e** 100% is used.

  'bedops **-e** 1' is also popular.

**-i**, **--intersect** File1 File2 \[File\]\*

**-m**, **--merge** File1 \[File\]\*

**-n**, **--not-element-of** \[bp \| percentage\] ReferenceFile File2 \[File\]\*

- by default, **-n** 100% is used.

  'bedops **-n** 1' is also popular.

**-p**, **--partition** File1 \[File\]\*

**-s**, **--symmdiff** File1 File2 \[File\]\*

**-u**, **--everything** File1 \[File\]\*

**-w**, **--chop** \[bp\] \[--stagger \<nt\>\] \[-x\] File1 \[File\]\*

-

  by default, **-w** 1 is used with no staggering.

Example: bedops **--range** 10 **-u** file1.bed

-

  NOTE: Only operations **-e**\|n\|u preserve all columns (no flattening)

## SEE ALSO

The full documentation for **bedops** is maintained as a Texinfo manual.  If the **info** and **bedops** programs are properly installed at your site, the command

-

  **info bedops**

should give you access to the complete manual.