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D: 15 Oct 2026

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General usage

Getting started

Flag usage summaries

Column set descriptors

Citation instructions

Standard data input

PLINK 1 binary (.bed)

PROVISIONAL_REF?

PLINK 2 binary (.pgen)

Autoconversion behavior

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

Oxford genotype (.bgen)

Oxford haplotype (.haps)

EIGENSOFT binary

BIMBAM Mean Genotype

23andMe text

PLINK 1 text (.ped, .tped)

PLINK 1 dosage

Sample ID conversion

Dosage import settings

Generate random

Unusual chromosome IDs

Recombination map

Allele frequencies

Phenotypes

Covariates

'Cluster' import

Variant sets

Reference genome (.fa)

Input filtering

Sample ID file

Variant ID file

Interval-BED file

Set membership

Attribute-based

--extract-col-cond

QUAL, FILTER, INFO

Chromosomes

SNPs only

Palindromic SNPs

Simple variant window

Multiple variant ranges

Deduplicate variants

Sample/variant thinning

Pheno./covar. condition

Missingness

Category subset

--keep-col-match

Missing genotypes

Same-indiv selection

Number of distinct alleles

Allele frequencies/counts

Hardy-Weinberg

Imputation quality

Mendel errors

Sex

Founder status

Relationships

Main functions

Data management

--make-[b]pgen/--make-bed

--export

--output-chr

--zero-cluster

--split-par/--merge-par

--set-me-missing

--set-all-var-ids

--recover-var-ids

--update-map...

--update-ids...

--flip

--flip-scan

--ref-allele

--ref-from-fa

--normalize

--indiv-sort

--write-covar

--variance-standardize

--quantile-normalize

--split-cat-pheno

--pheno-svd

--pmerge[-list]

--write-samples

--info-to-cols

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--test-mishap

--hardy

--mendel

--het

--check-sex/--impute-sex

--fst

--pgen-info

Pairwise diffs

--pgen-diff

--sample-diff

Linkage disequilibrium

--indep...

--r[2]-[un]phased

--ld

--ld-score

--show-tags

--blocks

Sample-distance matrices

Identity-by-state/Hamming

(--distance...)

Relationship/covariance

(--make-grm-bin...)

--make-king...

--king-cutoff

Runs of homozygosity

Population stratification

--pca

PCA projection

--neighbour

Association analysis

--glm

--glm ERRCODE values

--gwas-ssf

--test-missing

--adjust-file

Monte Carlo permutation

Family-based association

--tucc

Report postprocessing

--clump

--gene-report

--meta-analysis

Epistasis

--epistasis-boost

--epistasis

--twolocus

Linear scoring

--score[-list]

--variant-score

Distributed computation

Command-line help

Bundled utilities

ldsc

mtag

vcf_subset

Miscellaneous

Flag/parameter reuse

System resource usage

--loop-cats

.zst decompression

Pseudorandom numbers

Warnings as errors

.pgen validation

Resources

1000 Genomes phase 3

HGDP-CEPH

FASTA files

Errors and warnings

Output file list

Order of operations

Developer information

GitHub root

Python library

R library

Compilation

Adding new functionality

Discussion forums

Credits

File formats

Tutorials

Setup

Rules of Thumb

Data Exploration 1 — HWE, Allele Frequency Spectrum

Data Exploration 2 — Genomic Structure

Linkage

Relationship Matrix

Genome-Wide Assocation Analyses (GWAS)

Regressions

bcftools

Quick index search

Output file list

This is a brief list of all distinctive file extensions generated by PLINK 2.0, along with content summaries and links to the associated flag(s). See the file formats appendix for detailed specifications.

Extension	Source(s)	Contents
.*.<number>	--parallel	Partial result of distributed computation.
.acount	--freq counts	Allele count report (dosages considered).
.adjusted	--adjust, --adjust-file	Multiple-testing-corrected association analysis p-values.
.afreq	--freq	Allele frequency report (dosages considered).
.allele.no.snp	--update-alleles	Variants skipped due to mismatching old allele(s).
.aperm	--glm	Association analysis adaptive permutation test report.
.bcf	--export bcf[-4.2]	Variant Call Format (v4.2 or 4.3), binary form.
.beagle.dat	--export beagle-unphased	BEAGLE 3.3 unphased marker format.
.beagle.dat.phased	--export beagle-phased	BEAGLE 3.3 phased marker format.
.bed	--make-bed...	PLINK 1 binary biallelic genotype table. Could be sample-major.
.bgen	--export bgen...	Oxford variant information + genomic data binary file, v1.1-v1.3.
.bim	--make-bed...	PLINK 1 variant information file, part of binary fileset.
.bin	several	Matrix of binary floating point values.
.bins	--freq {ref,alt1}bins=	Allele count or frequency histogram.
.blocks*	--blocks	Estimated haplotype blocks.
.clumps	--clump	Reprocessed LD-clumped report.
.clumps.missing_allele	--clump	List of top (variant ID, A1) pairs skipped on account of A1.
.clumps.missing_id	--clump	List of top variant IDs missing from main dataset.
.cov	--write-covar...	Covariate table.
.dist	--distance	Sample distance matrix (allele-count units, text).
.eigenval	--pca	Principal component eigenvalues.
.eigenvec*	--pca	Principal component eigenvectors.
.epi.*	--epistasis [-boost]	Epistatic interaction scan reports.
.fam	--make-bed...	PLINK 1 sample information text file, part of binary fileset.
.flipscan*	--flip-scan	Strand inconsistency report.
.fst.summary	--fst	Between-population Wright's F_ST report.
.fst.var	--fst	Per-variant Wright's F_ST report for one population pair.
.gcount	--geno-counts	Genotype count report.
.gen	--export oxford	Oxford variant information + genomic data text file.
.gene.report	--gene-report	Reprocessed gene-based report.
.geno	--export eig[t]	EIGENSOFT binary biallelic genotype table.
.genopairs	--twolocus	Genotype-pair count table.
.glm.firth	--glm firth	Firth regression association statistics.
.glm.logistic	--glm no-firth	Logistic regression association statistics.
.glm.logistic.hybrid	--glm	Logistic/Firth hybrid regression association statistics.
.glm.multinomial*	--glm multinomial	Multinomial logistic/Firth regression association statistics.
.grm	--make-grm-list	GCTA relationship matrix (original format).
.grm.N.bin	--make-grm-bin	GCTA triangular binary observation count matrix.
.grm.bin	--make-grm-bin	GCTA triangular binary relationship matrix.
.grm.sp	--make-grm-sparse	GCTA sparse relationship matrix.
.*.gz	few	BGZipped file; use e.g. "gunzip <filename>" to unpack it.
.haps	--export haps...	Oxford phased haplotype file.
.hardy	--hardy	Hardy-Weinberg equilibrium exact test report (excludes chrX).
.hardy.x	--hardy	Graffelman-Weir chrX HWE exact test report.
.het	--het	Inbreeding coefficient report.
.hom	--homozyg	Run-of-homozygosity list.
.hom.indiv	--homozyg	Sample-based runs-of-homozygosity report.
.hom.summary	--homozyg	SNP-based runs-of-homozygosity report.
.*.id	lots	Ordered list of sample IDs associated with an analysis.
.ind	--export eig	EIGENSOFT sample information text file.
.indel	--list-23-indels	List of variants with 23andMe-style indel calls.
.info	--export HV[-1chr]	Haploview variant information file.
.kin0	--make-king-table	KING-robust kinship coefficient report.
.king	--make-king	KING-robust kinship coefficient matrix.
.ldscore*	--ld-score	Variant LD Scores.
.legend	--export hapslegend	Legend for Oxford .haps file with no header columns.
.lgen	--export lgen[-ref]	PLINK 1 long-format genomic data file.
.list	--export list	PLINK 1 genotype list file.
.map	--export ped	PLINK 1 text fileset variant information file.
.mdist	"--distance 1-ibs", --distance-matrix	Sample distance matrix (0-1 scale, text).
.*mendel	--mendel	Mendel error reports.
.meta	--meta-analysis	Meta-analysis.
.mgf	--export mgf	BIMBAM/GEMMA Mean Genotype Format.
.mibs	"--distance ibs", --ibs-matrix	Identity-by-state matrix (text).
.missing	--test-missing	Case/control nonrandom missingness test report.
.missing.hap	--test-mishap	Adjacent locus-based nonrandom missingness report.
.mperm	--glm	Association analysis max(T) permutation test report.
.neighbour	--neighbour	Nearest neighbor distance report.
.normalized	--normalize list	List of variants altered by --normalize.
.pdiff	--pgen-diff	Two-fileset genotype/dosage discordance report.
.ped	--export ped	PLINK 1 sample-major text pedigree + genotype file.
.pgen	--make-[b]pgen	PLINK 2 binary genomic data file.
.phase.inp	--export fastphase[-1chr]	fastPHASE genomic data file.
.phy	--export phylip[-phased]	Relaxed PHYLIP multiple sequence alignment format.
.pphe	--make-perm-pheno	Permuted phenotypes.
.prune.in	--indep...	Pruned set of variants in approximate LD.
.prune.out	--indep...	IDs of variants excluded by LD-based prune.
.psam	--make-pgen...	PLINK 2 sample information file, part of binary fileset.
.pvar	--make-pgen...	PLINK 2 variant information file, part of binary fileset.
.raw	--export {A,AD}	Sample-major text dosage file.
.recoverid.dup	--recover-var-ids	List of current variant IDs with multiple possible original IDs.
.rel	--make-rel	Relationship or covariance matrix.
.rlist	--export rlist	PLINK 1 rare genotype list file.
.rmdup.list	--rm-dup list	List of all duplicated variant IDs.
.rmdup.mismatch	--rm-dup	List of duplicate variant IDs with mismatched data.
.sample	--export	Oxford sample information text file.
.scount	--sample-counts	Sample variant-count report.
.sdiff	--sample-diff	Sample-pair discordance report.
.sdiff.summary	--sample-diff	Sample-pair discordance count summary.
.set	--write-set	Variant set membership list file.
.set.table	--set-table	Variant set membership table.
.sexcheck	--{check,impute}-sex	Sex imputation report.
.smiss	--missing	Sample-based missing data report.
.snp	--export eig	EIGENSOFT variant information text file.
.snplist	--write-snplist	List of variant IDs surviving filters/inclusion thresholds.
.sscore	--score[-list]	Sample scores.
.ssf.tsv	--gwas-ssf	Association statistics in GWAS-SSF format.
.strct.in	--export structure	Structure genomic data file.
.svd.pheno	--pheno-svd	Summary phenotypes generated via SVD.
.svd.pheno_wts	--pheno-svd	Singular values and right-singular vectors from phenotype SVD.
.tags*	--show-tags	Tagging variant list/report.
.tfam	--export tped	PLINK 1 sample information file, accompanied by .tped.
.tped	--export tped	PLINK 1 variant-major text variant information + genotype file.
.traw	--export Av	Variant-major text dosage file.
.tucc.*	--tucc	Pseudo case/control file(set).
.used_sites.tsv	--export used-sites	Variant information for relaxed-PHYLIP file.
.var.ranges	--write-var-ranges	Equal-size variant ranges.
.vcf	--export vcf[-4.2]	1000 Genomes Project Variant Call Format (v4.2 or 4.3).
.vcor	--r[2]-[un]phased	LD-statistic report.
.vcor1, .vcor2	--r[2]-[un]phased	Variant-correlation matrix.
.vinfo	--info-to-cols	INFO keys/values as a TSV.
.vmiss	--missing	Variant-based missing data report.
.vscore	--variant-score	Text variant score report.
.vscore.bin	--variant-score	Binary variant score file.
.vscore.cols	--variant-score	Column headers (score names) accompanying .vscore.bin.
.vscore.vars	--variant-score	Variant IDs accompanying .vscore.bin.
.*.zst	pack	Zstd-compressed file; can be unpacked with --zst-decompress.

Order of operations >>