bam2bedgraph command not found

Introduction

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

bam2bedgraph: command not found

or when using sudo you get the following error message

sudo: bam2bedgraph: command not found

Solutions to bam2bedgraph: command not found

How To Fix bam2bedgraph: command not found in Ubuntu / Debian / Kali Linux / Raspbian

In Ubuntu bam2bedgraph is provided by libbio-samtools-perl package.

libbio-samtools-perl is:

Bio::SamTools provides a Perl interface to the libbam library for indexed and unindexed SAM/BAM sequence alignment databases. It provides support for retrieving information on individual alignments, read pairs, and alignment coverage information across large regions. It also provides callback functionality for calling SNPs and performing other base-by-base functions. Most operations are compatible with the BioPerl Bio::SeqFeatureI interface, allowing BAM files to be used as a backend to the GBrowse genome browser application.

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

sudo apt-get -y install libbio-samtools-perl

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

You can also use apt command to install libbio-samtools-perl.

sudo apt -y install libbio-samtools-perl

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

sudo aptitude install libbio-samtools-perl

Summary

In this tutorial we learn how to fix bam2bedgraph command not found error in Ubuntu / Debian / Kali Linux or Raspbian distribution.