The latest source code can be downloaded from github using:

Note that if also the polysomy command should be included, the compilation instructions differ, see Optional Compilation with GSL below.

BCFtools and HTSlib depend on the zlib library http://zlib.net. Building them requires zlib development files to be installed on the build machine; you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux) or zlib-devel (on RPM/yum-based distributions) is installed.

cd to the bcftools directory containing the package’s source and type make to compile BCFtools.

If you already have a system-installed HTSlib or another HTSlib that you would prefer to build against, you can arrange this by overriding $(HTSDIR) by typing make HTSDIR=/path/to/htslib-source — see the Makefile for details.

The polysomy command depends on the GNU Scientific Library (GSL) and is not enabled by default. In order to compile it, type

Note that GSL is distributed under a GPL license, so when USE_GPL=1 is used to compile bcftools, the resulting program must only be distributed under terms compatible with that license.

In the default compilation mode the program is dual licensed and you may choose to be licensed under the terms of the MIT/Expat license or the GNU General Public License (GPL).

Type make install to install the bcftools executable and associated scripts and a manual page to /usr/local.

Type make prefix=/path/to/dir install to install everything under your choice of installation directory. The install target also understands DESTDIR and the other usual installation directory variables.

The bgzip and tabix utilities are provided by HTSlib. If you have not also installed HTSlib separately, you may wish to install these utilities by hand by copying bcftools/htslib/{bgzip,tabix} to the same bin directory to which you have installed bcftools et al.

We welcome your feedback, please help us improve this page by either opening an issue on github or editing it directly and sending a pull request.