HGDP+1KG Phased Reference Panel for Local Ancestry Inference (hg38)

Phased haplotypes from the joint 1000 Genomes Project (1KG) and Human Genome Diversity Project (HGDP) dataset, processed and QC'd for use as a reference panel in local ancestry inference (LAI) tools including RFMix v2, FLARE, and G-NOMIX. ## Original Data Source This dataset is derived from the gnomAD v3.1 HGDP+1KG joint callset: - **Source**: gnomAD (Genome Aggregation Database) - **URL**: https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg - **Google Cloud**: `gs://gcp-public-data--gnomad/resources/hgdp_1kg/phased_haplotypes_v2/` ## Processing Applied 1. Downloaded phased BCF files from gnomAD Google Cloud bucket 2. Filtered to biallelic SNPs only 3. Applied MAF > 0.5% filter 4. Renamed chromosomes to include 'chr' prefix for hg38 compatibility 5. Created per-chromosome VCF.gz files with CSI indices ## Samples - **Total samples**: 4,094 (929 HGDP + 3,165 1KG samples) - **Populations**: 80 populations across 7 continental groups - **Phasing**: SHAPEIT5 ## Usage These files are designed for use with the genotyping_pipeline (https://github.com/chrisrob3312/genotyping_pipeline) Module 7 ancestry estimation, but can be used with any LAI tool that accepts phased VCF input. ## Citation If you use this dataset, please cite: 1. **gnomAD v3.1**: Karczewski KJ, et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature. 2020;581(7809):434-443. DOI: 10.1038/s41586-020-2308-7 2. **HGDP**: Bergström A, et al. Insights into human genetic variation and population history from 929 diverse genomes. Science. 2020;367(6484):eaay5012. DOI: 10.1126/science.aay5012 3. **1000 Genomes**: 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015;526(7571):68-74. DOI: 10.1038/nature15393 4. Joint-called 1KG-HGDP Data Resource**: Koenig Z, Yohannes MT, Nkambule LL, et al. A harmonized public resource of deeply sequenced diverse human genomes. Genome Research. 2024. https://doi.org/10.1101/gr.278378.123 RELATED IDENTIFIERS (add as "References"): - DOI: 10.1038/s41586-020-2308-7 (gnomAD paper) - DOI: 10.1126/science.aay5012 (HGDP paper) - DOI: 10.1038/nature15393 (1000 Genomes paper) - URL: https://github.com/chrisrob3312/genotyping_pipeline (Related software) - URL: https://gnomad.broadinstitute.org/downloads#v3-hgdp-1kg (Source data)