Plink2

Introduction

Plink2 is a whole genome association analysis toolset.

For more information, please check its website: https://biocontainers.pro/tools/plink2 and its home page on Github.

Versions

2.00a2.3

Commands

plink2

Module

You can load the modules by:

module load biocontainers
module load plink2

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 Plink2 on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=plink2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers plink2

plink2 --bfile HapMap_3_r3_1 --freq --out HapMap_3_r3_1_out