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.

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/1.10.2/bcftools-1.10.2.tar.bz2

If you want 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 in 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-1.10.2.tar.bz2

$ cd bcftools-1.10.2/

$ ./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.

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References

1. Danecek, P., McCarthy, S., & Li, H. (2015). bcftools—utilities for variant calling and manipulating vcfs and bcfs.