Introduction, downloads

D: 16 May 2024

Recent version history

What's new?

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General usage

Getting started

Flag usage summaries

Column set descriptors

Citation instructions

Standard data input

PLINK 1 binary (.bed)

PLINK 2 binary (.pgen)

Autoconversion behavior

VCF/BCF (.vcf[.gz], .bcf)

Oxford genotype (.bgen)

Oxford haplotype (.haps)

PLINK 1 text (.ped, .tped)

PLINK 1 dosage

Sample ID conversion

Dosage import settings

Generate random

Unusual chromosome IDs

Allele frequencies



'Cluster' import

Reference genome (.fa)

Input filtering

Sample ID file

Variant ID file

Interval-BED file




SNPs only

Simple variant window

Multiple variant ranges

Deduplicate variants

Sample/variant thinning

Pheno./covar. condition


Category subset


Missing genotypes

Number of distinct alleles

Allele frequencies/counts


Imputation quality


Founder status

Main functions

Data management




















Basic statistics










Pairwise diffs



Linkage disequilibrium




Sample-distance matrices





Population stratification


PCA projection

Association analysis


--glm ERRCODE values



Report postprocessing


Linear scoring



Distributed computation

Command-line help


Flag/parameter reuse

System resource usage


.zst decompression

Pseudorandom numbers

Warnings as errors

.pgen validation


1000 Genomes phase 3


FASTA files

Errors and warnings

Output file list

Order of operations

Developer information

GitHub root

Python library

R library


Adding new functionality

Discussion forums


File formats

Quick index search


PLINK 2.0 alpha was developed by Christopher Chang with support from GRAIL, LLC and Human Longevity, Inc., and substantial input from Stanford's Department of Biomedical Data Science.

  • The .pgen file format is primarily an adaptation of ideas from SNPack (Francisco Sambo, Barbara Di Camillo, Gianna Toffolo, Claudio Cobelli) to more general contexts.
  • The KING-robust kinship estimation method was developed by Ani Manichaikul et al. at the University of Virginia.
  • The extended chrX Hardy-Weinberg equilibrium test was developed by Jan Graffelman (Universitat Politecnica de Catalunya) and Bruce Weir (University of Washington).
  • Christoph Lippert (Human Longevity), Manuel Rivas (Stanford), and Yosuke Tanigawa (Stanford) contributed significantly to development and testing of the Python and R file I/O libraries.
  • Firth logistic regression was added due to discussion with Manuel Rivas. The implementation is ported from Georg Heinze's logistf R package.
  • The Zstandard compression format and libraries used by PLINK 2.0 were developed by Yann Collet and Przemysław Skibiński, with support from Facebook, Inc.
  • The fast PCA approximation is ported from Kevin Galinsky's contribution to EIGENSOFT 6.
  • The array-popcount improvement is based on Faster Population Counts Using AVX2 Instructions by Wojciech Muła, Nathan Kurz, and Daniel Lemire, along with Kim Walisch's libpopcnt implementation.
  • The bgzip-decompression improvement is based on libdeflate (Eric Biggers), and htslib 1.8 integration work by James Bonfield.
  • Thanks to numerous other testers at GRAIL, Human Longevity, Stanford, and elsewhere for bug reports and helpful suggestions.

File format reference >>