Plink2
Introduction
Plink2 is a whole genome association analysis toolset.
For more information, please check:
BioContainers: https://biocontainers.pro/tools/plink2
Versions
2.00a2.3
Commands
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 -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=plink2
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module purge
module load plink2/XXXX ### you can run *module avail plink2* to check all available versions
plink2 --bfile HapMap_3_r3_1 --freq --out HapMap_3_r3_1_out