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kgp

1000 Genomes Project Metadata

Metadata about populations and data about samples from the 1000 Genomes Project, including the 2,504 samples sequenced for the Phase 3 release and the expanded collection of 3,202 samples with 602 additional trios. The data is described in Auton et al. (2015) <doi:10.1038/nature15393> and Byrska-Bishop et al. (2022) <doi:10.1016/j.cell.2022.08.004>, and raw data is available at <http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/>. See Turner (2022) <doi:10.48550/arXiv.2210.00539> for more details.

README

Code to download the data used in data-raw/kgp.R to create the package data:

```sh
cd inst/extdata
wget -Nq http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/20131219.populations.tsv
wget -Nq http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/20131219.superpopulations.tsv
wget -Nq http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20200731.ALL.ped
wget -Nq http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel
wget -Nq http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/20140625_related_individuals.txt
wget -Nq http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/20130606_g1k_3202_samples_ped_population.txt

# This doesn't work. Need to go to https://www.internationalgenome.org/data-portal/population to download.
# curl -kO http://www.internationalgenome.org/api/beta/population/_search/igsr_populations.tsv
```

Versions across snapshots

VersionRepositoryFileSize
1.1.1 rolling linux/jammy R-4.5 kgp_1.1.1.tar.gz 323.6 KiB
1.1.1 rolling linux/noble R-4.5 kgp_1.1.1.tar.gz 323.1 KiB
1.1.1 rolling source/ R- kgp_1.1.1.tar.gz 305.1 KiB
1.1.1 latest linux/jammy R-4.5 kgp_1.1.1.tar.gz 323.6 KiB
1.1.1 latest linux/noble R-4.5 kgp_1.1.1.tar.gz 323.1 KiB
1.1.1 latest source/ R- kgp_1.1.1.tar.gz 305.1 KiB
1.1.1 2026-04-26 source/ R- kgp_1.1.1.tar.gz 305.1 KiB
1.1.1 2026-04-23 source/ R- kgp_1.1.1.tar.gz 305.1 KiB
1.1.1 2026-04-09 windows/windows R-4.5 kgp_1.1.1.zip 321.0 KiB
1.1.1 2025-04-20 source/ R- kgp_1.1.1.tar.gz 305.1 KiB

Dependencies (latest)

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