samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

• Latest Version: 1.17
• Added: February, 2015
• Updated: March, 2025
• Link: http://www.htslib.org

Show all available versions:

$ module avail samtools

Load one version into your environment and run it:

$ module load samtools/1.17
$ samtools

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.17/samtools-1.17.tar.bz2
$ tar xf samtools-1.17.tar.bz2
$ cd samtools-1.17
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.17 --with-htslib=/export/apps/htslib/1.17
$ make
$ sudo mkdir -p /export/apps/samtools/1.17
$ sudo chown aorth /export/apps/samtools/1.17
$ make install
$ sudo chown -R root:root /export/apps/samtools/1.17

Note: this links against htslib/1.17, which is installed as a module. As of 1.17 this was compiled on CentOS 8 Stream.