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 calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

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.

Version

Type plink on command line

Sample session

First put the *.ped and *.map input files etc in the current directory.

% plink --file test
% plink --file test --freq
% plink --file test --assoc
% plink --file test --make-bed /home/user/plink/t1
@----------------------------------------------------------@
|        PLINK!       |     v1.03      |   04/Jun/2008     |
|----------------------------------------------------------|
|  (C) 2008 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Wed Jul  9 13:43:13 2008

Options in effect:
        --noweb
        --file test1

2 (of 2) markers to be included from [ test1.map ]
6 individuals read from [ test1.ped ] 
6 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
3 cases, 3 controls and 0 missing
6 males, 0 females, and 0 of unspecified sex
Before frequency and genotyping pruning, there are 2 SNPs
6 founders and 0 non-founders found
0 of 6 individuals removed for low genotyping ( MIND > 0.1 )
Total genotyping rate in remaining individuals is 1
0 SNPs failed missingness test ( GENO > 0.1 )
0 SNPs failed frequency test ( MAF < 0.01 )
After frequency and genotyping pruning, there are 2 SNPs
After filtering, 3 cases, 3 controls and 0 missing
After filtering, 6 males, 0 females, and 0 of unspecified sex

Analysis finished: Wed Jul  9 13:43:13 2008

@----------------------------------------------------------@
|        PLINK!       |     v1.03      |   04/Jun/2008     |
|----------------------------------------------------------|
|  (C) 2008 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Wed Jul  9 13:43:13 2008

Options in effect:
        --noweb
        --file test1
        --freq

2 (of 2) markers to be included from [ test1.map ]
6 individuals read from [ test1.ped ] 
6 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
3 cases, 3 controls and 0 missing
6 males, 0 females, and 0 of unspecified sex
Before frequency and genotyping pruning, there are 2 SNPs
6 founders and 0 non-founders found
0 of 6 individuals removed for low genotyping ( MIND > 0.1 )
Writing allele frequencies (founders-only) to [ plink.frq ] 

Analysis finished: Wed Jul  9 13:43:13 2008

@----------------------------------------------------------@
|        PLINK!       |     v1.03      |   04/Jun/2008     |
|----------------------------------------------------------|
|  (C) 2008 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Wed Jul  9 13:43:13 2008

Options in effect:
        --noweb
        --file test1
        --assoc

2 (of 2) markers to be included from [ test1.map ]
6 individuals read from [ test1.ped ] 
6 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
3 cases, 3 controls and 0 missing
6 males, 0 females, and 0 of unspecified sex
Before frequency and genotyping pruning, there are 2 SNPs
6 founders and 0 non-founders found
0 of 6 individuals removed for low genotyping ( MIND > 0.1 )
Total genotyping rate in remaining individuals is 1
0 SNPs failed missingness test ( GENO > 0.1 )
0 SNPs failed frequency test ( MAF < 0.01 )
After frequency and genotyping pruning, there are 2 SNPs
Writing main association results to [ plink.assoc ] 

Analysis finished: Wed Jul  9 13:43:13 2008


@----------------------------------------------------------@
|        PLINK!       |     v1.03      |   04/Jun/2008     |
|----------------------------------------------------------|
|  (C) 2008 Shaun Purcell, GNU General Public License, v2  |
|----------------------------------------------------------|
|  For documentation, citation & bug-report instructions:  |
|        http://pngu.mgh.harvard.edu/purcell/plink/        |
@----------------------------------------------------------@

Skipping web check... [ --noweb ] 
Writing this text to log file [ plink.log ]
Analysis started: Wed Jul  9 13:43:13 2008

Options in effect:
        --noweb
        --file test1
        --make-bed

2 (of 2) markers to be included from [ test1.map ]
6 individuals read from [ test1.ped ] 
6 individuals with nonmissing phenotypes
Assuming a disease phenotype (1=unaff, 2=aff, 0=miss)
Missing phenotype value is also -9
3 cases, 3 controls and 0 missing
6 males, 0 

Documentation

http://pngu.mgh.harvard.edu/~purcell/plink/