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: 1.6
• Added: February, 2015
• Updated: December, 2017
• Link: http://www.htslib.org

Show all available versions of samtools:

$ module avail samtools

Load a particular version of samtools:

$ module load samtools/1.6

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.6/samtools-1.6.tar.bz2
$ tar xf samtools-1.6.tar.bz2 
$ cd samtools-1.6
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.6
$ make all all-htslib
$ sudo mkdir /export/apps/samtools/1.6
$ sudo chown aorth /export/apps/samtools/1.6
$ make install install-htslib
$ sudo chown -R root:root /export/apps/samtools/1.6