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A simple library and CLI tool to manipulate BED files

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Build Status Docs Status JOSS Status DOI License: MIT


Bedparse is a simple python module and CLI tool to perform common operations on BED files.

It offers 11 sub-commands that implement the following functionality:

  • filter: Filtering of transcripts based on annotations
  • join: Joining of annotation files based on transcript names
  • gtf2bed: Conversion from GTF to BED format
  • convertChr: Conversion from UCSC to Ensembl chromosome names (and viceversa)
  • bed12tobed6: Conversion from bed12 to bed6
  • promoter: Promoter reporting
  • introns: Intron reporting
  • cds: CDS reporting
  • 3pUTR and 5pUTR: UTR reporting
  • validateFormat: Check that the file conforms with the BED format


Installing is as simple as:

pip install bedparse

Basic usage

The basic syntax in the form: bedparse subcommand [parameters].

For a list of all subcommands and a brief explanation of what they do, use: bedparse --help.

For a detailed explanation of each subcommand and a list of its parameters, use the --help option after the subcommand's name, e.g.: bedparse promoter --help


Our documentation is hosted on Read the Docs.

We also have a short tutorial to guide you through the basic functions.


If you use bedparse please cite the following paper:

Leonardi, (2019). Bedparse: feature extraction from BED files. Journal of Open Source Software, 4(34), 1228,

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