Processed Whole-Genome Variant Data (VCF) and Sample ID Lists for African and European Ancestry Cohorts

README – Processed Whole-Genome Variant DatasetThis dataset contains processed variant-level information derived from whole-genome sequencing (WGS) data generated from participants of the Louisiana Osteoporosis Study (LOS). The data are organized for multi-ancestry genomic analyses and include variant location and allele information for two ancestry groups: African ancestry (AFA) and European ancestry (CAU).Genomic DNA was extracted from peripheral blood samples and sequenced on the DNBSEQ-500 platform (BGI Americas) using 150-bp paired-end reads. Sequencing reads were aligned to the human reference genome GRCh38/hg38 using Burrows-Wheeler Aligner (BWA v0.7.12). Variant discovery followed the Genome Analysis Toolkit (GATK v4.0.3) Best Practices workflow with HaplotypeCaller, and variant quality score recalibration (VQSR) was applied to obtain high-confidence variants.Genotype data processing and quality control followed the GoDMC pipeline. Quality control was applied to autosomal chromosomes (1–22). Variants failing Hardy–Weinberg equilibrium (P 0.2. Individuals deviating more than 7 standard deviations from the mean along any principal component were considered ancestry outliers and removed. Principal components were recalculated after outlier removal.After quality control, 7,803,505 variants remained in the African ancestry cohort and 5,792,887 variants remained in the European ancestry cohort.The files distributed in this dataset contain variant-level genomic coordinates and allele information derived from the quality-controlled dataset and are intended for genomic annotation, reference panel harmonization, variant catalog comparison, and other population-level analyses.Files IncludedAFA_chr_all.vcf.gzVariant-level VCF file containing genomic positions and allele information for variants identified in individuals of African ancestry.CAU_chr_all.vcf.gzVariant-level VCF file containing genomic positions and allele information for variants identified in individuals of European ancestry.intersect_ids_AA.txtSample identifiers retained after quality control and cross-dataset intersection for the African ancestry cohort.intersect_ids_EA.txtSample identifiers retained after quality control and cross-dataset intersection for the European ancestry cohort.