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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 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 latest installed version of plink, simply load the plink module:

$ module load plink
$ plink --help
PLINK v1.90b4.6 64-bit (15 Aug 2017)           www.cog-genomics.org/plink/1.9/
(C) 2005-2017 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.

Example Jobs

Serial job

Here is an example job for plink version 1.9 using 4 cores with 2G memory per core.

#!/bin/bash
#$ -cwd
#$ -l h_vmem=2G
#$ -pe smp 4

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 using 4 cores with 2G memory per core.

#!/bin/bash
#$ -cwd
#$ -l h_vmem=2G
#$ -pe smp 4

module load plink/2.0-20170920

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