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: 1.11
• Added: February, 2015
• Updated: January, 2021
• Link: http://www.htslib.org

Show all available versions of samtools:

$ module avail samtools

Load a particular version of samtools into your environment and run it:

$ module load samtools/1.11
$ samtools

Notes from the sysadmin during installation:

$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.11/samtools-1.11.tar.bz2
$ tar xf samtools-1.11.tar.bz2
$ cd samtools-1.11
# install a newer compiler from Red Hat software collections
$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
$ scl enable devtoolset-7 bash
$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.11 --with-htslib=/export/apps/htslib/1.11
$ make
$ sudo mkdir -p /export/apps/samtools/1.11
$ sudo chown aorth /export/apps/samtools/1.11
$ make install
$ sudo chown -R root:root /export/apps/samtools/1.11

This links against htslib/1.11, which is installed as a module.