Introduction, downloads

S: 13 Feb 2017 (b3.46)

D: 13 Feb 2017

Recent version history

What's new?

Future development


Note to testers

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General usage

Citation instructions

Standard data input

PLINK 1 binary (.bed)

Autoconversion behavior

PLINK text (.ped, .tped...)

VCF (.vcf{.gz}, .bcf)

Oxford (.gen{.gz}, .bgen)

23andMe text

Generate random

Unusual chromosome IDs

Recombination map



Clusters of samples

Variant sets

Binary distance matrix

IBD report (.genome)

Input filtering

Sample ID file

Variant ID file

Cluster membership

Set membership



SNPs only

Simple variant window

Multiple variant ranges

Sample/variant thinning

Covariates (--filter)

Missing genotypes

Missing phenotypes

Minor allele frequencies


Mendel errors

Quality scores


Main functions

Data management

















Merge failures

VCF reference merge




Basic statistics









Linkage disequilibrium





Distance matrices






Distance-pheno. analysis





Population stratification





Association analysis

Basic case/control

  (--assoc, --model)

Stratified case/control

  (--mh, --mh2, --homog)

Quantitative trait

  (--assoc, --gxe)

Regression w/ covariates

  (--linear, --logistic)




Monte Carlo permutation

Set-based tests

REML additive heritability

Family-based association




Report postprocessing









Allelic scoring (--score)

R plugins (--R)

Secondary input

GCTA matrix (.grm.bin...)

Distributed computation

Command-line help


Tabs vs. spaces

Flag/parameter reuse

System resource usage

Pseudorandom numbers


1000 Genomes phase 1

Teaching materials

Gene range lists

Functional SNP attributes

Errors and warnings

Output file list

Order of operations

For developers

GitHub repository


Core algorithms

Partial sum lookup

Bit population count

Ternary dot product

Vertical population count

Exact statistical tests

Multithreaded gzip

Adding new functionality

Google groups




File formats

Quick index search

Output file list

This is a brief list of all file extensions generated by PLINK 1.9, 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.
.adjusted--adjustMultiple-testing-corrected association analysis p-values. mismatch report.
.annot--annotatePLINK report with position/variant ID-based annotations.
.assoc--assoc1df allelic chi-square C/C association analysis report.
.assoc.dosage--dosageDosage association analysis report (could be C/C or QT).
.assoc.fisher--assoc fisher{-midp}Association analysis report using Fisher p-values.
.assoc.linear--linearMulti-covariate quant. trait association analysis report.
.assoc.logistic--logisticMulti-covariate case/control association analysis report.
.auto.R--RR plugin function results.
.beagle.dat--recode beagle-nomapBEAGLE multi-chromosome sample + genome data file.
.bed--make-bed; --merge...PLINK binary biallelic genotype table.
.bed.vmaj(automatic)Variant-major .bed file (when input .bed is sample-major)
.bim--make-bed...; --merge...PLINK variant information file, part of binary fileset.
.*.binseveralMatrix of binary floating point values.
.blocks*--blocksEstimated haplotype blocks.
.chr-*.dat--recode beagleBEAGLE single-autosome sample + genome data file.
.chr-*.map--recode beagleBEAGLE single-autosome variant information file.
.clst--write-clusterPruned cluster list.
.clumped*--clumpReprocessed LD-clumped report.
.cluster*--clusterHierarchical clustering report.
.cmh--mh/--bdCochran-Mantel-Haenszel 2x2xK test report.
.cmh2--mh2Cochran-Mantel-Haenszel IxJxK test report.
.cnv.overlap--cnv-check-no-overlapOverlapping CNV segment report.
.cnv.summary--cfilePer-variant CNV summary.
.cov--write-covar...Covariate table.
.debug.R--R debugSequence of R commands --R would normally execute.
.dfam--dfamSib-TDT association report.
.diff--{b}mergeMerge conflict report from --merge-mode 6 or 7.
.dist--distanceTab-delimited allele count distance matrix.
.dupvar--list-duplicate-varsDuplicate-position-and-alleles variant report.
.eigenval--pcaPrincipal component eigenvalues.
.eigenvec*--pcaPrincipal component eigenvectors.
.epi.*--{fast-}epistasisEpistatic interaction scan reports.
.fam--make-bed...; --merge...PLINK sample information text file, part of binary fileset.
.flipscan*--flip-scanCase/control strand inconsistency report.
.frq--freqBasic allele frequency report. case-controlCase/control phenotype-stratified allele frequency report.
.frq.count--freq countsBasic allele count report.
.frq.strat--freqCluster-stratified allele frequency report.
.frqx--freqxPLINK 1.9 allele + heterozygote count report.
.fst--fstFixation index report.
.gen--recode oxfordOxford variant information + genomic data text file.
.genome--genomeIdentity-by-descent report.
.gplink--gplinkReserved for gPLINK. (Currently a simple error indicator.)
.grm--make-grm-gzGCTA relationship matrix (original format).
.grm.N.bin--make-grm-binGCTA triangular binary observation count matrix.
.grm.bin--make-grm-binGCTA triangular binary relationship matrix. --grm-gz + --rel-cutoff, a pruned set of sample IDs.
.*.gzpackGzipped file; use e.g. "gunzip [filename]" to unpack it.
.het--hetMethod-of-moments F coefficient estimates.
.hh(automatic)List of het. haploid and nonmale Ychr genotypes.
.hom--homozyg...Run-of-homozygosity list.
.hom.indiv--homozyg...Sample-based runs-of-homozygosity report.
.hom.overlap*--homozyg group...Overlapping ROH pool report.
.hom.summary--homozyg...SNP-based runs-of-homozygosity report.
.homog--homogChi-square partitioning odds ratio homogeneity report.
.hwe--hardyHardy-Weinberg equilibrium exact test statistic report.
.ibc--ibcGCTA inbreeding coefficient report.
.*.idlotsOrdered list of sample IDs associated with an analysis.
.imiss--missingSample-based missing data report.
.indel--list-23-indelsList of variants with 23andMe-style indel calls.
.info--recode HV{-1chr}Haploview variant information file.
.irem--mindIDs of samples excluded by --mind.
.lasso--lassoLASSO variant effect size estimates.
.ld--r/--r2Inter-variant correlation table or matrix.
.ldset--set-r2List of same-set marker pairs violating r2 threshold.
.lgen--recode lgen{-ref}PLINK long-format genomic data file.
.list--recode listGenotype list file.
.lmiss--missingVariant-based missing data report.
.map--recodePLINK text fileset variant information file.
.mdist--distance, --ibs-matrixSpace- or tab-delimited distance proportion matrix.
.mdist.missing--cluster missingSpace-delimited identity-by-missingness matrix.
.mds--mds-plotHaploview-friendly multidimensional scaling report.
.mds.eigvals--mds-plot eigvalsMultidimensional scaling eigenvalues.
.*mendel--mendelMendel error reports.
.mibs--distance, --ibs-matrixSpace- or tab-delimited IBS matrix.
.missing--test-missingCase/control nonrandom missingness test report.
.missing.hap--test-mishapAdjacent locus-based nonrandom missingness report.
.missnp--bmerge, --merge-listList of variants with more than two alleles.
.model--model5-test association analysis report.
.mperm--model...Association analysis max(T) permutation test report.
.nearest--neighbourNearest neighbor distance report.
.nopred--scoreList of (non-dosage) --score input file problems.
.nosex(automatic)List of samples with ambiguous sex codes.
.occur.dosage--dosage occurDosage data variant occurrence report.
.out.dosage--write-dosageMerged dosage data.
.ped--recodePLINK/Merlin/Haploview text sample + genome data file.
.perm--model...Association analysis adaptive permutation test report.
.pphe--make-perm-phenoPermuted phenotypes.
.prob--meta-analysisMeta-analysis rejected variant list.
.profile--scoreAllelic scoring results. set of markers in approximate LD.
.prune.out--indep...IDs of variants excluded by LD-based prune.
.qassoc--assocQuantitative phenotype association analysis report.
.qassoc.gxe--gxeQuantitative trait interaction report.
.qassoc.means--assocQuantitative trait means and SDs stratified by genotype.
.qfam--qfam...Family-based quantitative trait association report. gene-based report.
.raw--recode A{D}Additive + dominant component file.
.recode.*.txt--recode bimbam{-1chr}BIMBAM genomic data fileset.
.recode.phase.inp--recode fastphase{-1chr}fastPHASE genomic data file.
.recode.strct_in--recode structureStructure genomic data file.
.ref--recode lgen-refReference allele list accompanying .lgen fileset.
.rel--make-relTab-delimited relationship or covariance matrix., --rel-cutoffWith --rel-cutoff, a pruned set of unrelated sample IDs.
.rlist--recode rlistRare genotype list file.
.sample--recode oxfordOxford sample information text file.
.set--write-setVariant set membership list file.
.set.{m}perm--model...Set association permutation test report.
.set.table--set-tableVariant set membership table.
.sexcheck--check-sex...X chromosome-based sex validity report.
.simfreq--simulate{-qt}Realized simulated dataset parameters.
.skip.3allele--biallelic-onlyList of variant IDs filtered out due to 3+ alleles.
.snplist--write-snplistList of variant IDs surviving filters/inclusion thresholds.
.tags*--show-tagsTagging variant list/report.
.tdt--tdtTransmission disequilibrium test report.
.tdt.poo--tdt pooParent-of-origin analysis.
.tfam--recode transposePLINK sample information file, part of transposed fileset.
.tped--recode transposePLINK transposed text genotype table.
.traw--recode A-transposeVariant-major additive component file.
.twolocus--twolocus4x4 joint genotype count table.
.var.ranges--write-var-rangesEqual-size variant ranges.
.vcf--recode vcf...1000 Genomes Project Variant Call Format (v4.2).

Order of operations >>