PLINK is a whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

• Version: 2.00-alpha (Nov 28, 2019)
• Added: October, 2011
• Updated: December, 2019
• Link: https://www.cog-genomics.org/plink/2.0/

See versions of plink which are available:

$ module avail plink

Load one version into your environment and run it:

$ module load plink/2.00-alpha
$ plink2

Note: If you are running your job on a newer compute node like compute05 you can run plink2-avx2 instead of plink2 as that server has a newer CPU and can use a more optimized plink.

Notes from the sysadmin during installation:

$ cd /tmp
$ wget http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20191128.zip
$ sudo mkdir /export/apps/plink/2.00-alpha
$ sudo cp plink2 /export/apps/plink/2.00-alpha
$ rm plink2
$ wget http://s3.amazonaws.com/plink2-assets/plink2_linux_avx2_20191128.zip
$ unzip plink2_linux_avx2_20191128.zip
$ sudo cp plink2 /export/apps/plink/2.00-alpha/plink2-avx2

The AVX2 build only runs on compute05. The rest of our compute nodes are too old and must use the 64-bit builds.