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GenomicsSoftwareTools

Installing BCFtools on Ubuntu

Tariq Abdullah
Last updated: August 3, 2024 6:33 pm
Tariq Abdullah
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2 Min Read
Installing bcftools on Ubuntu
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BCFtools is a set of utilities that are used to manipulate variant call files (VCF) and binary call files (BCF). It can be used for both compressed and uncompressed sort of files. In this article, we will install BCFtools on Ubuntu.

Contents
Getting startedDownloading BCFtoolsInstalling prerequisitesInstalling BCFtoolsReferences

Getting started

Let’s update and upgrade the system first.

$ sudo apt-get update

$ sudo apt-get upgrade

Downloading BCFtools

Change to the directory where you want to download and install the software. Let’s say, Downloads. Open a terminal by pressing Ctrl+Alt+T and type the following commands:

$ cd Downloads/

$ wget https://github.com/samtools/bcftools/releases/download/1.20/bcftools-1.20.tar.bz2

If you wish to download it manually, then click here.

Installing prerequisites

Before installing BCFtools, you need to install the following libraries. Copy and paste the following command into your terminal.

$ sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libperl-dev libgsl0-dev

Installing BCFtools

We are in the same directory (i.e., Downloads). Now extract the downloaded package and install using the following commands.

$ tar xvjf bcftools-1.20.tar.bz2

$ cd bcftools-1.20/

$ ./configure

$ make

It will take a few minutes for a successful install. Check the installation by typing $ bcftools --version. If it displays the version, then you have successfully installed the BCFtools. To see the arguments, type $ bcftools --help.


References

  1. Danecek, P., McCarthy, S., & Li, H. (2015). bcftools—utilities for variant calling and manipulating vcfs and bcfs.
TAGGED:bcfbcftoolsgenomicsinstallationsamtoolsubuntuvcf
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ByTariq Abdullah
Tariq is founder of Bioinformatics Review and Lead Developer at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.
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