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Cloufield/GWASLab-Reference

GWASLab reference datasets Processed genomic reference files used by GWASLab (download_ref / gwaslab download ref). This dataset replaces the previous Dropbox hosting for GWASLab-processed panels. Official dbSNP VCFs, UCSC FASTA, Ensembl/RefSeq GTF, and liftOver chains stay at their original hosts. Package catalog: reference.json. Checksums for every file in this repo are in md5sum.txt. Download with GWASLab import gwaslab as gl gl.download_ref("1kg_eas_hg19")… See the full description on the dataset page: https://huggingface.co/datasets/Cloufield/GWASLab-Reference.

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GWASLab reference datasets

Processed genomic reference files used by GWASLab (download_ref / gwaslab download ref). This dataset replaces the previous Dropbox hosting for GWASLab-processed panels. Official dbSNP VCFs, UCSC FASTA, Ensembl/RefSeq GTF, and liftOver chains stay at their original hosts.

Package catalog: `reference.json`. Checksums for every file in this repo are in `md5sum.txt`.

Download with GWASLab

python

import gwaslab as gl

gl.download_ref("1kg_eas_hg19")
print(gl.get_path("1kg_eas_hg19"))

bash

gwaslab download ref 1kg_eas_hg19
gwaslab path 1kg_eas_hg19

Direct Hub URL (basename is the local filename download_ref writes):

https://huggingface.co/datasets/Cloufield/gwaslab-reference/resolve/main/1kg/hg19/EAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz

Layout

Path	GWASLab keyword(s)	Use
`1kg/hg19/*.vcf.gz` (+ `.tbi`)	`1kg_{afr,amr,eas,eur,pan,sas}_hg19`	LD / strand / AF (1KGP3v5, hg19)
`1kg/hg38/*.vcf.gz` (+ `.tbi`)	`1kg_{afr,amr,eas,eur,pan,sas}_hg38`	LD / strand / AF (1KG 30x, hg38)
`rsid/1kg_dbsnp151_*_auto.txt.gz`	`1kg_dbsnp151_hg19_auto`, `1kg_dbsnp151_hg38_auto`	SNPID–rsID tables (autosomes)
`eaf/PAN.hapmap3.*.EAF.tsv.gz`	`1kg_hm3_hg19_eaf`, `1kg_hm3_hg38_eaf`	HapMap3 EAF for ancestry
`recombination/recombination_hg*.tar.gz`	`recombination_hg19`, `recombination_hg38`	Regional recombination tracks
`examples/t2d_bbj.txt.gz`	(not a catalog keyword)	Tutorial BBJ T2D sumstats

Ancestries: AFR, AMR, EAS, EUR, SAS, PAN (all 1KG super-populations combined). Multi-allelic variants were decomposed and normalized; INFO includes population AF.

Processing

1KG VCFs were processed by GWASLab for regional LD plots and strand inference. They are not a substitute for the official 1000 Genomes release files.

Citations

—GWASLab: He Y, Koido M, Shimmori Y, Kamatani Y. GWASLab: a Python package for processing and visualizing GWAS summary statistics. Jxiv (2023). https://doi.org/10.51094/jxiv.305
—1000 Genomes Project: The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature (2015). 30x high-coverage data: Byrska-Bishop et al., Cell (2022).
—HapMap recombination maps: International HapMap Consortium.
—BBJ T2D example: Suzuki K et al. Identification of 28 new susceptibility loci for type 2 diabetes in the Japanese population. Nat Genet (2019). Source: http://jenger.riken.jp/

Redistribute and cite the original consortia terms for 1KG, HapMap, dbSNP-derived tables, and BBJ summary statistics.