Introduction, downloads

D: 1 Jul 2021

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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 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]

--pgen-diff

--write-samples

Basic statistics

--freq

--geno-counts

--sample-counts

--missing

--genotyping-rate

--hardy

--het

--fst

--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

--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

Errors and warnings

Output file list

Order of operations

Google groups

Credits

File formats

Quick index search

Resources

This page is under construction. If there's something you consider to be an essential PLINK resource which is not mentioned on this page, contact us and/or comment in the plink2-users Google group.

Genotype data

If you do not have another .zst decompressor installed, you can use plink2 for this purpose:

plink2 --zst-decompress chr1_phase3.pgen.zst > chr1_phase3.pgen

(Note that only the .pgen files need to be decompressed before use; plink2 can operate directly on .pvar.zst files.)

1000 Genomes phase 3, phased and annotated

These files contain all relevant information in the final data release's reference-build-37 genotype VCFs (last modification on 5 May 2016). (Quick start: just download the three boldfaced links, and then decompress the .pgen.zst.)

We've been informed that Dropbox is partially blocked in mainland China, as well as some workplaces. If this prevents you from downloading the files below, contact us for access to an alternate source.

Refer to the 1000 Genomes website for additional sample information, data usage rules, and citation instructions.

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