Introduction, downloads

D: 28 Oct 2018

Recent version history

What's new?

Coming next

General usage

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

Phenotypes

Covariates

'Cluster' import

Reference genome (.fa)

Input filtering

Sample ID file

Variant ID file

Interval-BED file

QUAL, FILTER, INFO

Chromosomes

SNPs only

Simple variant window

Multiple variant ranges

Deduplicate variants

Sample/variant thinning

Pheno./covar. condition

Missingness

Category subset

--keep-fcol (was --filter)

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

--ref-allele

--ref-from-fa

--normalize

--indiv-sort

--write-covar

--variance-standardize

--quantile-normalize

--split-cat-pheno

--write-samples

(TBD)

Resources

1000 Genomes phase 3

Output file list

Order of operations

Credits

File formats

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 genotype VCFs (last modification on 19 Apr 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. 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.

Output file list >>