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Plink

Plink is a whole genome association analysis tool set, designed to perform large scale computationally analyses.

Plink is available as a module on Apocrita.

Versions

There are two major versions of Plink on Apocrita 1.9 and the updated version 2.0. The differences between the versions are listed here.

Version warning

Plink version 1.9 is a beta version. Plink version 2.0 is an alpha version.

Binary naming differences

  • Plink version 1.9 using plink binary.
  • Plink version 2.0 using plink2 binary.

Usage

To run the default installed version of plink, simply load the plink module:

$ module load plink
$ plink2 --help
PLINK v2.00a3.3LM 64-bit Intel (3 Jun 2022)    www.cog-genomics.org/plink/2.0/
(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3

Core Usage

To ensure that plink uses the correct number of cores, the --threads ${NSLOTS} option should be used.

Array Jobs

If you submit an array job that runs plink, please set a conservative task concurrency value such as 1 or 2 to prevent your job from overloading the cluster.

Example jobs

Serial jobs

Here is an example job for plink version 1.9 running on 4 cores and 8GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load plink/1.9-170906

plink --threads ${NSLOTS} \
      --silent \
      --dummy 387 1112 0.03 scalar-pheno \
      --out dummy1

plink --threads ${NSLOTS} \
      --bfile dummy1 \
      --recode \
      --out dummy1.new_recode

Here is an example job for Plink version 2.0 running on 4 cores and 8GB of memory:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 4
#$ -l h_rt=1:0:0
#$ -l h_vmem=2G

module load plink

plink2 --threads ${NSLOTS} \
      --dummy 387 1112 0.03 scalar-pheno \
      --out dummy1

plink2 --threads ${NSLOTS} \
      --pfile dummy1 \
      --export vcf \
      --freq \
      --keep-autoconv \
      --out dummy1.new_recode

References