D: 20 Feb 2019

Main functions

(TBD)

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.

• 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 (2.25 GiB), .pvar.zst (1.28 GiB), unannotated .pvar.zst (613.6 MiB)
• No-singletons merged dataset (usable with 8 GiB RAM): .pgen.zst (2.13 GiB), .pvar.zst (835.3 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.

Output file list >>