Current releases

SAMtools and BCFtools are distributed as individual packages. The code uses HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

HTSlib is also distributed as a separate package which can be installed if you are writing your own programs against the HTSlib API. HTSlib also provides the bgzip, htsfile, and tabix utilities, so you may also want to build and install HTSlib to get these utilities, or see the additional instructions in INSTALL to install them from a samtools or bcftools source package.

Download current source releases:   samtools-1.3.1 bcftools-1.3.1 htslib-1.3.2

See also release notes for samtools, bcftools, and htslib.

New releases are announced on the samtools mailing lists and by @htslib on Twitter. Previous releases are available from the samtools GitHub organisation (see samtools, bcftools, or htslib releases) or from the samtools Sourceforge project.

Building and installing

Building each desired package from source is very simple:

cd samtools-1.x    # and similarly for bcftools and htslib
make
make prefix=/where/to/install install

See INSTALL in each of the source directories for further details.

The executable programs will be installed to a bin subdirectory under your specified prefix, so you may wish to add this directory to your $PATH:

export PATH=/where/to/install/bin:$PATH    # for sh or bash users
setenv PATH /where/to/install/bin:$PATH    # for csh users

Historical SAMtools/BCFtools 0.1.x releases

Prior to the introduction of HTSlib, SAMtools and BCFtools were distributed in a single samtools-0.1.x package. These old versions remain available from the Sourceforge samtools project.