PLINK

Policy

PLINK is freely available to users at HPC2N.

Description

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.

The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data).

PLINK (one syllable) is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with the support of others.

Availability

On HPC2N we have PLINK available as a module on Akka and Abisko. Binaries are compiled for serial usage, with LAPACK, but without support for webcheck and R.

Usage at HPC2N

To use the plink module, add it to your environment:

module add plink

Loading the module should set any needed environmental variables as well as the path.

See http://pngu.mgh.harvard.edu/~purcell/plink/ for more information about the usage of plink.

Akka:

Make a batch-script similar to this example:

#!/bin/bash
# Project to run under
#PBS -A SNICXXX-YY-ZZ
# Name of job script 
#PBS -N My_plink_job
# name of the output file
#PBS -o My_plink_job.out
# name of the error file
#PBS -e My_plink_job.err
# when to send email
#PBS -m ae

# asking for 1 node, 8 processors 
#PBS -l nodes=1:ppn=1
# the job may to use up to 30 minutes to run
#PBS -l walltime=00:30:00

# change to the directory the job was submitted from
cd $PBS_O_WORKDIR

# Load the PLINK module 
module load plink 

# run the job
plink <options>

Submit it with

qsub <jobscript>

where <jobscript> is the name you give your batch-script.

Abisko:

Make a job-script similar to this example:

#!/bin/bash
# Project to run under
#SBATCH -A SNICXXX-YY-ZZ
# name of the error file
#SBATCH --error=my_plink_job_%J.err
# name of the output file
#SBATCH --output=my_plink_job_%J.out
# when to send email
#SBATCH --mail-type=ALL

# asking for 1 node, 8 processors 
#SBATCH -N 1
#SBATCH -n 8 
# the job may to use up to 30 minutes to run
#SBATCH -t 00:30:00

# Load the PLINK module 
module load plink 

# run the job
plink <options>