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: 1.3.1
• Updated: February, 2017
• Added: February, 2015
• Link: http://www.htslib.org/

Show all available versions of samtools:

$ module avail samtools

Load a particular version of samtools:

$ module load samtools/1.3.1

Notes from the sysadmin during installation:

$ cd /tmp
$ wget -qO- "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" | tar xjv
$ cd samtools-1.3.1/
$ scl enable devtoolset-2 bash
$ sudo mkdir /export/apps/samtools/1.3.1
$ sudo chown -R joguya:joguya /export/apps/samtools/1.3.1
$ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 --prefix=/export/apps/samtools/1.3.1
$ make all install-htslib
$ make install install-htslib
$ sudo chown -R root:root /export/apps/samtools/1.3.1