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D: 14 Aug 2022
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General usage
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Standard data input
PLINK 1 binary (.bed)
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VCF/BCF (.vcf[.gz], .bcf)
Oxford genotype (.bgen)
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--extract-col-cond
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--make-[b]pgen/--make-bed
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--update-map...
--update-ids...
--ref-allele
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--write-covar
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--split-cat-pheno
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--write-samples
Basic statistics
--freq
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Pairwise diffs
--pgen-diff
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Linkage disequilibrium
--indep...
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Sample-distance matrices
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(--make-grm-bin...)
--make-king...
--king-cutoff
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PCA projection
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1000 Genomes phase 3
HGDP-CEPH
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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.
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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 .
Callset:
2019-05-16 main release
2019-05-16 statistically phased subset
(source) (source)
Split by chromosome?
hgdp_all.pgen.zst hgdp_all.pvar.zst hgdp_all_noannot.pvar.zst hgdp.psam
Common sample information file: hgdp.psam
Remove "_noannot" from the .pvar.zst filenames before use.
hgdp_chr1.pgen.zst hgdp_chr1.pvar.zst hgdp_chr1_noannot.pvar.zst hgdp_chr2.pgen.zst hgdp_chr2.pvar.zst hgdp_chr2_noannot.pvar.zst hgdp_chr3.pgen.zst hgdp_chr3.pvar.zst hgdp_chr3_noannot.pvar.zst hgdp_chr4.pgen.zst hgdp_chr4.pvar.zst hgdp_chr4_noannot.pvar.zst hgdp_chr5.pgen.zst hgdp_chr5.pvar.zst hgdp_chr5_noannot.pvar.zst hgdp_chr6.pgen.zst hgdp_chr6.pvar.zst hgdp_chr6_noannot.pvar.zst hgdp_chr7.pgen.zst hgdp_chr7.pvar.zst hgdp_chr7_noannot.pvar.zst hgdp_chr8.pgen.zst hgdp_chr8.pvar.zst hgdp_chr8_noannot.pvar.zst hgdp_chr9.pgen.zst hgdp_chr9.pvar.zst hgdp_chr9_noannot.pvar.zst hgdp_chr10.pgen.zst hgdp_chr10.pvar.zst hgdp_chr10_noannot.pvar.zst hgdp_chr11.pgen.zst hgdp_chr11.pvar.zst hgdp_chr11_noannot.pvar.zst hgdp_chr12.pgen.zst hgdp_chr12.pvar.zst hgdp_chr12_noannot.pvar.zst hgdp_chr13.pgen.zst hgdp_chr13.pvar.zst hgdp_chr13_noannot.pvar.zst hgdp_chr14.pgen.zst hgdp_chr14.pvar.zst hgdp_chr14_noannot.pvar.zst hgdp_chr15.pgen.zst hgdp_chr15.pvar.zst hgdp_chr15_noannot.pvar.zst hgdp_chr16.pgen.zst hgdp_chr16.pvar.zst hgdp_chr16_noannot.pvar.zst hgdp_chr17.pgen.zst hgdp_chr17.pvar.zst hgdp_chr17_noannot.pvar.zst hgdp_chr18.pgen.zst hgdp_chr18.pvar.zst hgdp_chr18_noannot.pvar.zst hgdp_chr19.pgen.zst hgdp_chr19.pvar.zst hgdp_chr19_noannot.pvar.zst hgdp_chr20.pgen.zst hgdp_chr20.pvar.zst hgdp_chr20_noannot.pvar.zst hgdp_chr21.pgen.zst hgdp_chr21.pvar.zst hgdp_chr21_noannot.pvar.zst hgdp_chr22.pgen.zst hgdp_chr22.pvar.zst hgdp_chr22_noannot.pvar.zst hgdp_chrX.pgen.zst hgdp_chrX.pvar.zst hgdp_chrX_noannot.pvar.zst hgdp_chrY.pgen.zst hgdp_chrY.pvar.zst hgdp_chrY_noannot.pvar.zst
hgdp_statphase.pgen.zst hgdp_statphase.pvar.zst hgdp.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 hgdp_all.pgen.zst > hgdp_all.pgen
This dataset was aligned to GRCh38, and variant calls were made on the autosomes, chrX, and chrY. There are 929 samples, with no 1st-degree relations. Samples have been sorted by ID.
The dataset contains (unsplit) multiallelic variants, and one variant on chrY which isn't left-normalized . ~6.57% of genotype calls are missing.
The 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 was aligned to GRCh38, and variant calls were made on only the autosomes. There are 929 samples, with no 1st-degree relations. Samples have been sorted by ID.
The dataset contains (unsplit) multiallelic variants, and ~4.27% of genotype calls are missing. All variants are left-normalized.
This data is freely available with no restrictions on the types of analyses that can be carried out. If you use this data in a publication, please cite Bergström et al. (2020) Insights into human genetic variation and population history from 929 diverse genomes. Science, 367.
Refer to the paper and the Fondation Jean Dausset-CEPH website for more information about this dataset.
These are the reference genomes that the aforementioned 1000 Genomes and HGDP samples were aligned against. Note that --fa can directly read these compressed files.
Errors and warnings >>