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: 1.5
• Added: February, 2015
• Updated: June, 2017
• Link: http://www.htslib.org

Show all available versions of samtools:

$ module avail samtools

Load a particular version of samtools:

$ module load samtools/1.5

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2
$ tar xf samtools-1.5.tar.bz2
$ cd samtools-1.5
$ scl enable devtoolset-4 bash
$ sudo mkdir /export/apps/samtools/1.5
$ sudo chown aorth /export/apps/samtools/1.5
$ ./configure --enable-plugins --enable-libcurl --without-curses --prefix=/export/apps/samtools/1.5
$ make all all-htslib
$ make install install-htslib
$ sudo chown -R root:root /export/apps/samtools/1.5