Introduction, downloads

D: 16 May 2024

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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

Output file list

This is a brief list of all 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.

.*.<number>--parallelPartial result of distributed computation.
.acount--freq countsAllele count report (dosages considered).
.adjusted--adjust, --adjust-fileMultiple-testing-corrected association analysis p-values.
.afreq--freqAllele frequency report (dosages considered).
.bcf--export bcf[-4.2]Variant Call Format (v4.2 or 4.3), binary form.
.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.
.binseveralMatrix of binary floating point values.
.bins--freq {ref,alt1}bins=Allele count or frequency histogram.
.clumps--clumpReprocessed LD-clumped report.
.clumps.missing_allele--clumpList of top (variant ID, A1) pairs skipped on account of A1.
.clumps.missing_id--clumpList of top variant IDs missing from main dataset.
.cov--write-covar...Covariate table.
.eigenval--pcaPrincipal component eigenvalues.
.eigenvec*--pcaPrincipal component eigenvectors.
.fam--make-bed...PLINK 1 sample information text file, part of binary fileset.
.fst.summary--fstBetween-population Wright's FST report.
.fst.var--fstPer-variant Wright's FST report for one population pair.
.gcount--geno-countsGenotype count report.
.gen--export oxfordOxford variant information + genomic data text file.
.glm.firth--glm firthFirth regression association statistics.
.glm.logistic--glm no-firthLogistic regression association statistics.
.glm.logistic.hybrid--glmLogistic/Firth hybrid regression association statistics.
.grm--make-grm-listGCTA relationship matrix (original format).
.grm.N.bin--make-grm-binGCTA triangular binary observation count matrix.
.grm.bin--make-grm-binGCTA triangular binary relationship matrix.
.*.gzfewBGZipped file; use e.g. "gunzip <filename>" to unpack it.
.haps--export haps...Oxford phased haplotype file.
.hardy--hardyHardy-Weinberg equilibrium exact test report (excludes chrX).
.hardy.x--hardyGraffelman-Weir chrX HWE exact test report.
.het--hetInbreeding coefficient report.
.*.idlotsOrdered list of sample IDs associated with an analysis.
.kin0--make-king-tableKING-robust kinship coefficient report.
.king--make-kingKING-robust kinship coefficient matrix.
.legend--export hapslegendLegend for Oxford .haps file with no header columns.
.map--export pedPLINK 1 text fileset variant information file.
.normalized--normalize listList of variants altered by --normalize.
.pdiff--pgen-diffTwo-fileset genotype/dosage discordance report.
.ped--export pedPLINK 1 sample-major text pedigree + genotype file.
.pgen--make-[b]pgenPLINK 2 binary genomic data file.
.phy--export phylip[-phased]Relaxed PHYLIP multiple sequence alignment format. set of variants in approximate LD.
.prune.out--indep-pairwiseIDs 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-idsList of current variant IDs with multiple possible original IDs.
.rel--make-relRelationship or covariance matrix.
.rmdup.list--rm-dup listList of all duplicated variant IDs.
.rmdup.mismatch--rm-dupList of duplicate variant IDs with mismatched data.
.sample--exportOxford sample information text file.
.scount--sample-countsSample variant-count report.
.sdiff--sample-diffSample-pair discordance report.
.sdiff.summary--sample-diffSample-pair discordance count summary.
.smiss--missingSample-based missing data report.
.snplist--write-snplistList of variant IDs surviving filters/inclusion thresholds.
.sscore--score[-list]Sample scores.
.ssf.tsv--gwas-ssfAssociation statistics in GWAS-SSF format.
.svd.pheno--pheno-svdSummary phenotypes generated via SVD.
.svd.pheno_wts--pheno-svdSingular values and right-singular vectors from phenotype SVD.
.tfam--export tpedPLINK 1 sample information file, accompanied by .tped.
.tped--export tpedPLINK 1 variant-major text variant information + genotype file.
.traw--export AvVariant-major text dosage file.
.used_sites.tsv--export used-sitesVariant information for relaxed-PHYLIP file.
.vcf--export vcf[-4.2]1000 Genomes Project Variant Call Format (v4.2 or 4.3).
.vcor--r[2]-[un]phasedLD-statistic report.
.vcor1, .vcor2--r[2]-[un]phasedVariant-correlation matrix.
.vmiss--missingVariant-based missing data report.
.vscore--variant-scoreText variant score report.
.vscore.bin--variant-scoreBinary variant score file.
.vscore.cols--variant-scoreColumn headers (score names) accompanying .vscore.bin.
.vscore.vars--variant-scoreVariant IDs accompanying .vscore.bin.
.*.zstpackZstd-compressed file; can be unpacked with --zst-decompress.

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