Introduction, downloads

D: 5 Feb 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

Google groups


File formats

Quick index search

Google groups

To be informed about updates, get technical support, make feature requests, and/or engage in other public communication about PLINK-related matters, you'll want to join one or two of our Google groups.

  • The plink2-announce group is the low-traffic choice, with nothing but major release announcements.
  • The plink2-users group is the general discussion and technical support forum. With luck, the archives will become useful over time as solutions to the most common issues accumulate. Release announcements will be crossposted here; we may also solicit feedback re: upcoming features.
  • plink2-dev is for those working with the source code. If you want to implement something new and/or perform a useful refactoring, this is a good place to discuss it, especially if you want to see your work merged into the main codebase; we'll try to answer your questions in enough detail to enable you to finish your job.

Credits >>