Introduction, downloads

D: 13 Dec 2019

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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 (.vcf[.gz])

Oxford genotype (.bgen)

Oxford haplotype (.haps)

PLINK 1 dosage

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

--write-samples

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--hardy

--pgen-info

Linkage disequilibrium

--indep...

--ld

Sample comparison

Sample-distance matrices

Relationship/covariance

  (--make-grm-bin...)

--make-king...

--king-cutoff

Population stratification

--pca

PCA projection

Association analysis

--glm

--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

Errors and warnings

Output file list

Order of operations

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).
.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.
.gcount--geno-countsGenotype count report.
.gen--export oxfordOxford variant information + genomic data text file.
.glm.firth--glm firthFirth regression association statistics.
.glm.logistic--glmLogistic regression association statistics.
.glm.logistic.hybrid--glm firth-fallbackLogistic/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.
.*.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.
.normalized--normalize listList of variants altered by --normalize.
.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.
.traw--export A-transposeVariant-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.

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