Introduction, downloads
D: 23 Sep 2020
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What's new?
Coming next
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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
--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.
Common sample information file (not for chrY/chrM): original , pedigree-corrected
Raw KING-robust output (filtered to 2nd-degree relationships), 1st-degree --remove ID list , 1st+2nd-degree --remove ID list Merged dataset (excludes extra chrM samples, requires 12 GiB RAM to work with): .pgen.zst .pvar.zst unannotated .pvar.zst (613.6 MiB)No-singletons merged dataset (usable with 8 GiB RAM): .pgen.zst (2.13 GiB), .pvar.zst (812.4 MiB), unannotated .pvar.zst (361.9 MiB)
Split by chromosome:
chr1: .pgen.zst (172.2 MiB), .pvar.zst (100.4 MiB), unannotated .pvar.zst (47.5 MiB)
chr2: .pgen.zst (185.4 MiB), .pvar.zst (109.9 MiB), unannotated .pvar.zst (52 MiB)
chr3: .pgen.zst (153.4 MiB), .pvar.zst (90.6 MiB), unannotated .pvar.zst (42.9 MiB)
chr4: .pgen.zst (150.3 MiB), .pvar.zst (89.1 MiB), unannotated .pvar.zst (42.2 MiB)
chr5: .pgen.zst (136.4 MiB), .pvar.zst (81.6 MiB), unannotated .pvar.zst (38.8 MiB)
chr6: .pgen.zst (136 MiB), .pvar.zst (78.4 MiB), unannotated .pvar.zst (36.9 MiB)
chr7: .pgen.zst (130.6 MiB), .pvar.zst (73.5 MiB), unannotated .pvar.zst (34.6 MiB)
chr8: .pgen.zst (121.3 MiB), .pvar.zst (71.2 MiB), unannotated .pvar.zst (33.7 MiB)
chr9: .pgen.zst (102.6 MiB), .pvar.zst (55.6 MiB), unannotated .pvar.zst (26.2 MiB)
chr10: .pgen.zst (111.4 MiB), .pvar.zst (62.3 MiB), unannotated .pvar.zst (29.3 MiB)
chr11: .pgen.zst (106.5 MiB), .pvar.zst (62.7 MiB), unannotated .pvar.zst (29.7 MiB)
chr12: .pgen.zst (106 MiB), .pvar.zst (59.8 MiB), unannotated .pvar.zst (28.2 MiB)
chr13: .pgen.zst (78.4 MiB), .pvar.zst (44.6 MiB), unannotated .pvar.zst (21 MiB)
chr14: .pgen.zst (73.6 MiB), .pvar.zst (41.4 MiB), unannotated .pvar.zst (19.5 MiB)
chr15: .pgen.zst (71.6 MiB), .pvar.zst (38 MiB), unannotated .pvar.zst (17.9 MiB)
chr16: .pgen.zst (79.8 MiB), .pvar.zst (42 MiB), unannotated .pvar.zst (19.8 MiB)
chr17: .pgen.zst (68.2 MiB), .pvar.zst (36.4 MiB), unannotated .pvar.zst (17.1 MiB)
chr18: .pgen.zst (65.2 MiB), .pvar.zst (35.4 MiB), unannotated .pvar.zst (16.8 MiB)
chr19: .pgen.zst (57.6 MiB), .pvar.zst (28.9 MiB), unannotated .pvar.zst (13.5 MiB)
chr20: .pgen.zst (52.5 MiB), .pvar.zst (28.2 MiB), unannotated .pvar.zst (13.3 MiB)
chr21: .pgen.zst (34.6 MiB), .pvar.zst (17.4 MiB), unannotated .pvar.zst (8.08 MiB)
chr22: .pgen.zst (35.8 MiB), .pvar.zst (17.4 MiB), unannotated .pvar.zst (8.2 MiB)
chrX: .pgen.zst (73 MiB), .pvar.zst (44.7 MiB), unannotated .pvar.zst (18.3 MiB)
chrY: .pgen.zst (325 KiB), .pvar.zst (605 KiB), unannotated .pvar.zst (240.5 KiB), .psam
chrM: .pgen.zst (50.4 KiB), .pvar.zst (15.7 KiB), unannotated .pvar.zst (10.4 KiB), original .psam , pedigree-corrected .psam
Refer to the 1000 Genomes website for additional sample information , data usage rules , and citation instructions .
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