hlnicholls/postgwas-db-grch38-2025-11

nf-postgwas databases

Dataset repository for the hlnicholls/nf-postgwas pipeline

This repository provides reference resources required by the nf-postgwas workflow, a modular post-GWAS analysis pipeline for variant-to-gene mapping, fine-mapping, functional annotation, and gene prioritisation.

All data included here are publicly available and redistributed in their original form (or lightly reformatted for compatibility).
No individual-level genetic or patient data are contained in this repository.

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🧬 Contents

Folder	Description	Source / Version
1000genomes	1000 Genomes Project reference genotypes used for LD and fine-mapping.	1000 Genomes Phase 3 (public FTP)
ClinGen	Curated dosage-sensitivity and clinical gene annotations.	ClinGen, January 2024 release
coloc_gwas	GWAS summary statistics prepared for colocalisation analyses.	Curated public GWAS datasets (various sources)
dgidb	Drug–gene interaction database used for druggability annotations.	DGIdb v2024-12
gene_damage_index	Gene-level intolerance scores used in prioritisation.	Gene Damage Index (GDI) database
genetic_map	Genetic recombination maps used for fine-mapping and MAGMA inputs.	HapMap / 1000 Genomes recombination maps
gtex_v8_data	GTEx v8 tissue-specific eQTL and expression reference files.	GTEx Portal, release v8
hic	Hi-C chromatin contact maps from Jung et al., Nature Genetics 2019.	Jung et al. 2019, PMC6778519
HIPred	HI-Pred gene haploinsufficiency predictions.	HIPred (Zhao et al.)
impc	Mouse phenotyping and knockout data for gene function validation.	IMPC, release 2025-04-16
ldsc	LD Score Regression reference files.	Bulik-Sullivan et al. 2015 resources
MAGMA	Gene-mapping and annotation reference files for MAGMA.	MAGMA v1.10 public data
opentargets	Open Targets gene–trait and drug association data.	Open Targets v25.06
pops	PoPS gene-prioritisation model reference weights and gene features.	Finucane Lab PoPS (GitHub release)
plink	Reference PLINK binary data used for LD and locus-based operations.	1000 Genomes reference plink files
regulomedb	Regulatory annotation tracks for SNP-level functional evidence.	RegulomeDB public release

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🧭 Purpose

These databases provide all external dependencies required by nf-postgwas to perform:

• Locus compilation, distance-based pruning, and LD calculation
• Fine-mapping and colocalisation
• Variant annotation and regulatory mapping
• Gene prioritisation and drug-target enrichment

They ensure reproducibility and offline compatibility for users of the public Docker image
postgwas-pipeline.

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📁 Structure and Size

• Approximate total size: 42 GB
• Format: mostly .tsv, .txt, .bed, .gz, and .RData
• Each subdirectory contains only pre-processed reference data; no intermediate workflow results are included.

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📜 Licensing & Attribution

All resources are publicly available.
Each sub-dataset retains its original license and citation requirements.
Users should cite the original data sources as listed in the table above and in any derived publications.

Example citations:

• GTEx Consortium. Science 2020;369(6509):1318–1330.
• Jung et al. Nature Genetics 2019;51:1442–1452.
• ClinGen Consortium. Nucleic Acids Res. 2023;51(D1):D1364–D1373.
• DGIdb 4.0. Nucleic Acids Res. 2024;52(D1):D308–D314.

This dataset is provided for reproducibility and educational use only.

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🔗 Related Projects

• Pipeline: hlnicholls/nf-postgwas
• Container: Docker Hub: hlnicholls/postgwas-pipeline

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