bedpeToBam command not found

Introduction

When you run more command in linux terminal / console, you get the following error message

bedpeToBam: command not found

or when using sudo you get the following error message

sudo: bedpeToBam: command not found

Solutions to bedpeToBam: command not found

How To Fix bedpeToBam: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu bedpeToBam is provided by bedtools package.

bedtools is:

The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by streaming several BEDTools together.

The groupBy utility is distributed in the filo package.

To fix this problem, we can install more using the command below.

sudo apt-get -y install bedtools

This command might take some time to finish depending on your machine internet connection.

You can also use apt command to install bedtools.

sudo apt -y install bedtools

Or if you have aptitude installed you can use the following command.

sudo aptitude install bedtools

Summary

In this tutorial we learn how to fix bedpeToBam command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.