Variant Calling (Part 11): Population-Scale Genotyping Using gVCF and Joint Variant Calling
· 21 min read
Population-scale variant calling is a critical step in building genomic population projects. While single-sample variant calling is well established, scaling joint genotyping to thousands of WGS samples introduces challenges in performance, storage, and incremental updates. In this blog, I explore gVCF-based joint variant calling approaches and evaluate scalable solutions using modern open-source tools. I also discuss practical architecture considerations to efficiently construct population-scale genomics projects.