Genotyping Pipeline Reference Data v1.0
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Genotyping Pipeline - Reference Data Overview This Zenodo repository contains pre-built reference files for the Genotyping Pipeline, a Nextflow-based workflow for genotype imputation, quality control, and ancestry inference. Files Included 1. TOPMed PASS Variants Reference (3.8 GB) File: PASS.Variants.TOPMed_freeze10_hg38.tab.gz Pre-formatted variant summary from BRAVO TOPMed Freeze 10, containing only PASS-filtered variants (756M variants) in Rayner/McCarthy format for use with the HRC-1000G-check-bim.pl strand-checking script. Format (8 columns): CHR POS ID REF ALT AC AN AF 1 10019 rs775809821 TA T 6 301798 1.98823e-05 1 10039 rs978760828 A C 8 301798 2.65097e-05 ... Usage: Pre-imputation QC to check strand alignment and identify problematic variants. Option 2: Manual Download # Download directly from Zenodo wget https://zenodo.org/records/XXXXXXX/files/PASS.Variants.TOPMed_freeze10_hg38.tab.gz # Place in resources directory mv PASS.Variants.TOPMed_freeze10_hg38.tab.gz resources/rayner/ Data Sources File Source License TOPMed PASS Variants BRAVO Public summary statistics 1KG Reference 1000 Genomes Fort Lauderdale Agreement HGDP Reference HGDP Public Citation If you use this data, please cite: This pipeline: Magyar C, et al. (2025). Genotyping Pipeline: A Nextflow workflow for genotype imputation and ancestry inference. Zenodo. https://doi.org/10.5281/zenodo.18022757 TOPMed: Taliun D, et al. (2021). Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature, 590(7845), 290-299. 1000 Genomes: The 1000 Genomes Project Consortium. (2015). A global reference for human genetic variation. Nature, 526(7571), 68-74. Related Resources GitHub Repository: https://github.com/chrisrob3312/genotyping_pipeline Documentation: https://github.com/chrisrob3312/genotyping_pipeline/wiki Containers (Sylabs): library://chrisrob3312/genotyping_pipeline Version History Version Date Changes 1.0.0 2025-12-22 Initial release with TOPMed PASS variants Contact For questions or issues: Open an issue on GitHub Email: [christina.magyar@bcm.edu] License The reference data files are provided under their original licenses (see Data Sources above).
