Plink

Introduction

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

For more information, please check:
BioContainers: https://biocontainers.pro/tools/plink
Home page: https://zzz.bwh.harvard.edu/plink/

Versions

1.90b6.21

Commands

plink
prettify

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run plink on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=plink
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load plink/XXXX ### you can run *module avail plink* to check all available versions

plink --file toy --freq --out toy_analysis