Introduction, downloads

D: 14 Aug 2022

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General usage

Getting started

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

Phenotypes

Covariates

'Cluster' import

Reference genome (.fa)

Input filtering

Sample ID file

Variant ID file

Interval-BED file

--extract-col-cond

QUAL, FILTER, INFO

Chromosomes

SNPs only

Simple variant window

Multiple variant ranges

Deduplicate variants

Sample/variant thinning

Pheno./covar. condition

Missingness

Category subset

--keep-col-match

Missing genotypes

Number of distinct alleles

Allele frequencies/counts

Hardy-Weinberg

Imputation quality

Sex

Founder status

Main functions

Data management

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

--export

--output-chr

--split-par/--merge-par

--set-all-var-ids

--recover-var-ids

--update-map...

--update-ids...

--ref-allele

--ref-from-fa

--normalize

--indiv-sort

--write-covar

--variance-standardize

--quantile-normalize

--split-cat-pheno

--pmerge[-list]

--write-samples

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--hardy

--het

--fst

--pgen-info

Pairwise diffs

--pgen-diff

--sample-diff

Linkage disequilibrium

--indep...

--ld

Sample-distance matrices

Relationship/covariance

  (--make-grm-bin...)

--make-king...

--king-cutoff

Population stratification

--pca

PCA projection

Association analysis

--glm

--glm ERRCODE values

--adjust-file

Linear scoring

--score

--variant-score

Distributed computation

Command-line help

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

Compilation

Adding new functionality

Google groups

Credits

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.

ExtensionSource(s)Contents
.*.<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.
.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.
.prune.in--indep-pairwisePruned 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--scoreSample scores.
.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.
.vcf--export vcf[-4.2]1000 Genomes Project Variant Call Format (v4.2 or 4.3).
.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.

Order of operations >>