Introduction, downloads
D: 19 May 2022
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General usage
Getting started
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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
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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
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--loop-cats
.zst decompression
Pseudorandom numbers
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.pgen validation
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1000 Genomes phase 3
FASTA files
Errors and warnings
Output file list
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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.
The linked files are currently hosted by Dropbox. If you are unable to download them, contact us for access to an alternate source; we understand that Dropbox is blocked in some locations.
Genotype data
Callset:
2021-07-12 NYGC (build 38, 3202 samples, contigs unphased)
2016-05-05 primary release (build 37, 2504 samples)
(main source , chrY/chrM/contigs source )
(source)
Split by chromosome?
Keep singleton variants? (more info...) (hide info)
The no-singleton dataset can be a good starting point if you were planning on filtering out low-MAF variants anyway, or you're constrained to ≤ 8 GiB of workspace memory.
INFO annotations?
KING-based pedigree corrections? (more info...) (hide info)
The KING-robust algorithm is very effective at identifying 1st-degree relations within a population, and its output can also be used to distinguish between parent-child vs. sibling relationships — IBS0 is much higher for the latter, all other things being equal. One relationship previously flagged by KING-robust (NA20317-NA20318) was formally acknowledged to be a probable clerical error, and added to the official pedigree on 2020-07-31. (phase3_orig.psam does not contain this relationship, since it is based on the 2016-05-05 snapshot of the official pedigree.)
all_hg38.pgen.zst --allow-extra-chr )all_hg38_ns.pgen.zst --allow-extra-chr )all_phase3.pgen.zst all_phase3_ns.pgen.zst all_hg38.pvar.zst all_hg38_noannot.pvar.zst all_hg38_ns.pvar.zst all_hg38_ns_noannot.pvar.zst all_phase3.pvar.zst all_phase3_noannot.pvar.zst all_phase3_ns.pvar.zst all_phase3_ns_noannot.pvar.zst hg38_corrected.psam hg38_orig.psam phase3_corrected.psam phase3_orig.psam (rename to "all_hg38.psam" before use)
(rename to "all_hg38_ns.psam" before use)
(rename to "all_phase3.psam" before use)
(rename to "all_phase3_ns.psam" before use)
Common sample information file (not for chrY/chrM) :
hg38_corrected.psam hg38_orig.psam phase3_corrected.psam phase3_orig.psam chr1_hg38.psam, chr2_hg38.psam,
chr1_phase3.psam, chr2_phase3.psam,
etc. to this (or make a bunch of copies).
Remove "_noannot" from the .pvar.zst filenames before use.
chr1_hg38.pgen.zst chr1_hg38.pvar.zst chr1_hg38_noannot.pvar.zst chr2_hg38.pgen.zst chr2_hg38.pvar.zst chr2_hg38_noannot.pvar.zst chr3_hg38.pgen.zst chr3_hg38.pvar.zst chr3_hg38_noannot.pvar.zst chr4_hg38.pgen.zst chr4_hg38.pvar.zst chr4_hg38_noannot.pvar.zst chr5_hg38.pgen.zst chr5_hg38.pvar.zst chr5_hg38_noannot.pvar.zst chr6_hg38.pgen.zst chr6_hg38.pvar.zst chr6_hg38_noannot.pvar.zst chr7_hg38.pgen.zst chr7_hg38.pvar.zst chr7_hg38_noannot.pvar.zst chr8_hg38.pgen.zst chr8_hg38.pvar.zst chr8_hg38_noannot.pvar.zst chr9_hg38.pgen.zst chr9_hg38.pvar.zst chr9_hg38_noannot.pvar.zst chr10_hg38.pgen.zst chr10_hg38.pvar.zst chr10_hg38_noannot.pvar.zst chr11_hg38.pgen.zst chr11_hg38.pvar.zst chr11_hg38_noannot.pvar.zst chr12_hg38.pgen.zst chr12_hg38.pvar.zst chr12_hg38_noannot.pvar.zst chr13_hg38.pgen.zst chr13_hg38.pvar.zst chr13_hg38_noannot.pvar.zst chr14_hg38.pgen.zst chr14_hg38.pvar.zst chr14_hg38_noannot.pvar.zst chr15_hg38.pgen.zst chr15_hg38.pvar.zst chr15_hg38_noannot.pvar.zst chr16_hg38.pgen.zst chr16_hg38.pvar.zst chr16_hg38_noannot.pvar.zst chr17_hg38.pgen.zst chr17_hg38.pvar.zst chr17_hg38_noannot.pvar.zst chr18_hg38.pgen.zst chr18_hg38.pvar.zst chr18_hg38_noannot.pvar.zst chr19_hg38.pgen.zst chr19_hg38.pvar.zst chr19_hg38_noannot.pvar.zst chr20_hg38.pgen.zst chr20_hg38.pvar.zst chr20_hg38_noannot.pvar.zst chr21_hg38.pgen.zst chr21_hg38.pvar.zst chr21_hg38_noannot.pvar.zst chr22_hg38.pgen.zst chr22_hg38.pvar.zst chr22_hg38_noannot.pvar.zst chrX_hg38.pgen.zst chrX_hg38.pvar.zst chrX_hg38_noannot.pvar.zst chrY_hg38.pgen.zst chrY_hg38.pvar.zst chrY_hg38_noannot.pvar.zst chrM_hg38.pgen.zst chrM_hg38.pvar.zst chrM_hg38_noannot.pvar.zst contigs_hg38.pgen.zst contigs_hg38.pvar.zst contigs_hg38_noannot.pvar.zst
chr1_phase3.pgen.zst chr1_phase3.pvar.zst chr1_phase3_noannot.pvar.zst chr2_phase3.pgen.zst chr2_phase3.pvar.zst chr2_phase3_noannot.pvar.zst chr3_phase3.pgen.zst chr3_phase3.pvar.zst chr3_phase3_noannot.pvar.zst chr4_phase3.pgen.zst chr4_phase3.pvar.zst chr4_phase3_noannot.pvar.zst chr5_phase3.pgen.zst chr5_phase3.pvar.zst chr5_phase3_noannot.pvar.zst chr6_phase3.pgen.zst chr6_phase3.pvar.zst chr6_phase3_noannot.pvar.zst chr7_phase3.pgen.zst chr7_phase3.pvar.zst chr7_phase3_noannot.pvar.zst chr8_phase3.pgen.zst chr8_phase3.pvar.zst chr8_phase3_noannot.pvar.zst chr9_phase3.pgen.zst chr9_phase3.pvar.zst chr9_phase3_noannot.pvar.zst chr10_phase3.pgen.zst chr10_phase3.pvar.zst chr10_phase3_noannot.pvar.zst chr11_phase3.pgen.zst chr11_phase3.pvar.zst chr11_phase3_noannot.pvar.zst chr12_phase3.pgen.zst chr12_phase3.pvar.zst chr12_phase3_noannot.pvar.zst chr13_phase3.pgen.zst chr13_phase3.pvar.zst chr13_phase3_noannot.pvar.zst chr14_phase3.pgen.zst chr14_phase3.pvar.zst chr14_phase3_noannot.pvar.zst chr15_phase3.pgen.zst chr15_phase3.pvar.zst chr15_phase3_noannot.pvar.zst chr16_phase3.pgen.zst chr16_phase3.pvar.zst chr16_phase3_noannot.pvar.zst chr17_phase3.pgen.zst chr17_phase3.pvar.zst chr17_phase3_noannot.pvar.zst chr18_phase3.pgen.zst chr18_phase3.pvar.zst chr18_phase3_noannot.pvar.zst chr19_phase3.pgen.zst chr19_phase3.pvar.zst chr19_phase3_noannot.pvar.zst chr20_phase3.pgen.zst chr20_phase3.pvar.zst chr20_phase3_noannot.pvar.zst chr21_phase3.pgen.zst chr21_phase3.pvar.zst chr21_phase3_noannot.pvar.zst chr22_phase3.pgen.zst chr22_phase3.pvar.zst chr22_phase3_noannot.pvar.zst chrX_phase3.pgen.zst chrX_phase3.pvar.zst chrX_phase3_noannot.pvar.zst chrY_phase3.pgen.zst chrY_phase3.pvar.zst chrY_phase3_noannot.pvar.zst chrY_phase3.psam chrM_phase3.pgen.zst chrM_phase3.pvar.zst chrM_phase3_noannot.pvar.zst chrM_phase3_corrected.psam chrM_phase3_orig.psam
Notes:
.pgen.zst file(s) must be decompressed before use. (This isn't necessary for .pvar.zst files: see --pfile's 'vzs' modifier .) If you don't have another .zst decompressor installed, you can use PLINK 2 for this purpose:plink2 --zst-decompress all_hg38.pgen.zst > all_hg38.pgen
In addition to ~600 trios which were intentionally included, this dataset contains a few close relations which are not described in the .psam file, e.g. sibships where neither parent was sequenced. Use --remove with one of the following ID lists when you don't want close relations:--king-cutoff 0.177" and "--king-cutoff 0.0884", respectively. If you're curious, here's the --make-king-table + --king-table-filter report listing all 1st/2nd-degree related sample pairs: deg2_hg38.kin0
This dataset was intended to contain only unrelated samples; unfortunately, a few parent-child pairs, sibships, and second-degree relationships snuck in. Use --remove with one of the following ID lists when you don't want close relations:--king-cutoff 0.177" and "--king-cutoff 0.0884", respectively. If you're curious, here's the --make-king-table + --king-table-filter report listing all 1st/2nd-degree related sample pairs: deg2_phase3.kin0
This dataset fuses results from two different pipelines. The primary chr1..chrX genotypes are phased, contain no missing calls, and only have biallelic left-normalized variants (multiallelic variants were "split"). The chrY/chrM/contigs genotypes are unphased, contain some missing calls, multiallelic variants there are unsplit, and there are a few variants which aren't left-normalized .
All relevant information in the original phased chr1..chrX callset is preserved. The chrY/chrM/contigs source material contains per-genotype AD, DP, GQ, and PL fields which cannot be represented by the .pgen file format, and are consequently not preserved.
This dataset contains (unsplit) multiallelic variants, and a few variants which aren't left-normalized .
Refer to the 1000 Genomes website for additional sample information , data usage rules , and citation instructions .
These are the reference genomes that the aforementioned 1000 Genomes samples were aligned against. Note that --fa can directly read these compressed files.
Errors and warnings >>