PLINK¶

PLINK is a whole genome association analysis toolset. The plink bundle has three variants one for version 1.07, one for version 1.90b6.21, and one for version 2.00a3.7.

UFS HPC Usage Example¶

PLINK 1.9 is the default variant and can be used by running the following command the terminal:

1	`module load plink`

Add release=1.07 to the previous command to use PLINK 1.07:

module load plink release=1.07

Add release=2 to the previous command to use PLINK 2:

module load plink release=2

Once the variant is loaded the PLINK commands can be run as shown below, first example is for PLINK 1.07 and 1.9, and the second example is for PLINK 2:

plink

plink2

The plink_shell command can be run for a shell in the plink bundle.

1	`plink_shell`

Performance Notes¶

No performance notes available

Recommended resources per session¶

No recommended resources available

Benchmarks¶

No benchmarks available.

UFS HPC Community Guides and Tutorials¶

No community guides available.

Official site and documentation¶

PLINK 1.07¶

PLINK 1.9¶

PLINK 2¶

Licensing Information¶

PLINK 1.07 is licensed under the GPLv2 License, PLINK 1.9 is licensed under the GPLv3 license, and PLINK 2 is licensed under the GPLv3 license.

Primary citation¶

External Guides and Resources¶

If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za