SeqArray GDS Files for 1000 Genomes Project

SeqArray GDS Files for 1000 Genomes Project

If you have any question about SeqArray GDS file format, please send emails to Dr. Xiuwen Zheng:

1000 Genomes Project Phase 3 (on hg19):

The VCF files were downloaded from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502, and used for the file conversion.

Autosomes (2.4GB, 2504 individuals and 81,271,745 variants):
1KG_ALL.autosomes.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.gds
Chromosome X (86.8MB, 2504 individuals and 3,468,093 variants):
1KG_ALL.chrX.phase3_shapeit2_mvncall_integrated_v1b.20130502.genotypes.gds
Chromosome Y (2.4MB, 1233 males and 62,042 variants):
1KG_ALL.chrY.phase3_integrated_v2a.20130502.genotypes.gds
Chromosome MT (65KB, 2534 individuals and 3892 variants):
1KG_ALL.chrMT.phase3_callmom-v0_4.20130502.genotypes.gds

1000 Genomes Project Phase 3 (on GRCh38):

The VCF files were downloaded from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000_genomes_project/release/20190312_biallelic_SNV_and_INDEL, and used for the file conversion.

Chromosome 1, ..., 22, X (1.8GB, 2548 individuals and 78,229,218 variants):
ALL.allchr.shapeit2_integrated_snvindels_v2a_27022019.GRCh38.phased.gds

1000 Genomes High-coverage (30x) Project (on GRCh38):

The VCF files were downloaded from http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV, and used for the file conversion.

Chromosome 1, ..., 22, X (2.5GB, 3202 individuals and 73,554,796 variants):
1kGP_high_coverage_Illumina.allchr.filtered.SNV_INDEL_SV_phased_panel.gds
Reference: https://doi.org/10.1016/j.cell.2022.08.004

Other Datasets:

HapMap Project