## Study overview

Study Abbreviation: 1000G

Study Name: 1000 Genomes Project

Study Description: [The 1000 Genomes Project Web Site](https://www.internationalgenome.org/)

## Data Use Limitations

No restrictions

## Data included in workspace

This workspace contains two different callsets of 1000 genomes data: 

1. Phase 3 low-coverage sequencing of 2504 samples
2. High-coverage sequencing of 3202 samples

Each callset has data in the following formats:

1. VCF files for all populations combined, per chromosome (23 files, chroms 1-22 and X)
2. PLINK2 files for all populations combined, with all chromosomes (3 files, pgen/psam/pvar)
3. PLINK2 files per population and chromosome, subset to HapMap3 or MEGA+HapMap3 SNPs (chroms 1-22, ALL x SNP sets hm3, mega+hm3 x pgen/psam/pvar = 138 files) * (26 populations + 5 superpopulations). These files can be used as input for [simulation workflows](https://dockstore.org/organizations/PRIMED/collections/simulation).
4. File with list of samples related to other samples in the dataset at a threshold >= 2nd degree, as estimated by KING. Exclude samples from this list to establish an unrelated dataset.

### Sequencing Files

Links to each sequencing data file can be found in the `sequencing_file` table. The following identifiers may be useful for finding the desired data:

Phase 3 low-coverage sequencing of 2504 samples

Populations | Variant Set | `sample_set_id` | `sequencing_datset_id` | File Types
--- | --- | --- | --- | ---
All samples from all populations combined | All | phase3_2504_samples | f2bb0d1a | VCF (per chrom), PLINK2 (all chrom)
Population or superpopulation unrelated subsets | Subset to HapMap3 | \<POP\>_phase3_unrelated | \<POP\>_hg19_hm3 | PLINK2 (per chrom, all chrom)
Population or superpopulation unrelated subsets | Subset to MEGA + HapMap3 | \<POP\>_phase3_unrelated | \<POP\>_hg19_mega_hm3 | PLINK2 (per chrom, all chrom)


High-coverage sequencing of 3202 samples

Populations | Variant Set | `sample_set_id` | `sequencing_datset_id` | File Types
--- | --- | --- | --- | ---
All samples from all populations combined | All | all_3202_samples | d41f784b | VCF (per chrom), PLINK2 (all chrom)
Population or superpopulation unrelated subsets | Subset to HapMap3 | \<POP\>_highcov_unrelated | \<POP\>_hg38_hm3 | PLINK2 (per chrom, all chrom)
Population or superpopulation unrelated subsets | Subset to MEGA + HapMap3 | \<POP\>_highcov_unrelated | \<POP\>_hg38_mega_hm3 | PLINK2 (per chrom, all chrom)




### Details on data source

Low-coverage Phase 3 VCF files are hosted in a [public Google bucket](https://console.cloud.google.com/storage/browser/terra-featured-workspaces/GWAS/1kg-genotypes/vcf).

High-coverage VCF files are from the [1000 Genomes ftp site](https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/).

1000 Genomes data in PLINK2 format was obtained from the [PLINK2 website](https://www.cog-genomics.org/plink/2.0/resources#phase3_1kg).
These files were processed to partition the dataset by populations and subset SNPs.

## Data model

This workspace was prepared by the [PRIMED consortium](https://primedconsortium.org/) and conforms to the [PRIMED data model](https://github.com/UW-GAC/primed_data_models/).
 Platform: AnVIL

ANVIL_1000G_PRIMED_data_model

Description

Dataset Details