Add dataset card, checksums, EAF, rsID tables, recombination maps, and example sumstats

README.md

@@ -1,5 +1,64 @@
 ---
+pretty_name: GWASLab Reference
 license: other
-license_name: license
-license_link: LICENSE
+license_name: source-data-terms
+task_categories:
+  - other
+tags:
+  - gwas
+  - genomics
+  - 1000-genomes
+  - hapmap
+  - ld-reference
+  - allele-frequency
 ---
+
+# GWASLab reference datasets
+
+Processed genomic reference files used by [GWASLab](https://cloufield.github.io/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`](https://github.com/Cloufield/gwaslab/blob/main/src/gwaslab/data/reference.json). Checksums for every file in this repo are in [`md5sum.txt`](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.

eaf/PAN.hapmap3.hg19.EAF.tsv.gz

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eaf/PAN.hapmap3.hg38.EAF.tsv.gz

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examples/t2d_bbj.txt.gz

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md5sum.txt

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+# 1KG hg19 VCF
+b486381ac2e475381e8184b2c7c165e4  1kg/hg19/AFR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
+f9daa2144063c327006e4cffcae21510  1kg/hg19/AMR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
+6162a93cb80935168c0bfa519748b054  1kg/hg19/EAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
+2c78cb84cb1f90b576510decc45e5b9b  1kg/hg19/EUR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
+8f9eca55f9fc25e2a58a013a1ae0a9af  1kg/hg19/PAN.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
+fdf1c9831d74ae8e9c3960865cf7c22c  1kg/hg19/SAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz
+
+# 1KG hg38 VCF
+f1e0657ee7549915e5bde2f6324b0e57  1kg/hg38/AFR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz
+f4109fc1e23c0eb62762caaf4bed24d5  1kg/hg38/AMR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz
+5360451ef7f31cb44471144e427e6cfe  1kg/hg38/EAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz
+9e1aa56d8b843fef724b67e23932c95b  1kg/hg38/EUR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz
+32e160c40d5463befff35ab6e1310349  1kg/hg38/PAN.ALL.split_norm_af.1kg_30x.hg38.vcf.gz
+59fbbf0f30a7ad2f13a04b035e5dc373  1kg/hg38/SAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz
+
+# tabix indexes
+1a49d63b73fc1cc243bb1932b6c7690d  1kg/hg19/AFR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz.tbi
+2eea9760f51c62c234935bd0a9b12e6b  1kg/hg19/AMR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz.tbi
+0851e30153abe5ce8caefadbd421b678  1kg/hg19/EAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz.tbi
+3f0dec75d1c4ead3fb6dbee83696e3b8  1kg/hg19/EUR.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz.tbi
+02deef47840eee2beb81bb91098a0517  1kg/hg19/PAN.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz.tbi
+e13f282d76fe62b58f67cc9ac88e8440  1kg/hg19/SAS.ALL.split_norm_af.1kgp3v5.hg19.vcf.gz.tbi
+41caa99dc9ef1760a2aef7592c474d5f  1kg/hg38/AFR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz.tbi
+d2fb51f54951708b08a4986c50705c1b  1kg/hg38/AMR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz.tbi
+81991f2229546b6aff0a54abf6215ef7  1kg/hg38/EAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz.tbi
+37682637bc74ac49e98a317d063800eb  1kg/hg38/EUR.ALL.split_norm_af.1kg_30x.hg38.vcf.gz.tbi
+4bdf8242ae376dc3d6ba16e6e2dbcfa0  1kg/hg38/PAN.ALL.split_norm_af.1kg_30x.hg38.vcf.gz.tbi
+237438ed7ff2862ab43fb138f712aabc  1kg/hg38/SAS.ALL.split_norm_af.1kg_30x.hg38.vcf.gz.tbi
+
+# rsID tables
+7d1e7624fb6e4df7a2f6f05558d436b4  rsid/1kg_dbsnp151_hg19_auto.txt.gz
+4c7ef2d2415c18c286219e970fdda972  rsid/1kg_dbsnp151_hg38_auto.txt.gz
+
+# HapMap3 EAF
+ee95afbfb1899849f91fdb55fae8e567  eaf/PAN.hapmap3.hg19.EAF.tsv.gz
+6d41ce4af02711a532c19f1b1a5911c2  eaf/PAN.hapmap3.hg38.EAF.tsv.gz
+
+# recombination maps
+038255f22a8664d44f9fb907cfec3f4e  recombination/recombination_hg19.tar.gz
+dbeca47a92cfff4fd13aa217e21957e3  recombination/recombination_hg38.tar.gz
+
+# example sumstats
+67f9d8f49e75a8e2a9d38edf8800ebb9  examples/t2d_bbj.txt.gz

recombination/recombination_hg19.tar.gz

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recombination/recombination_hg38.tar.gz

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