Whole Genome Sequencing (WGS) is a powerful approach for studying genetic variations across the entire genome, providing insights into mutations, structural variants, and disease associations. GATK (Genome Analysis Toolkit) is a widely used tool for processing WGS data, offering pipelines for alignment, quality control, variant calling, and filtering. Genome-Wide Association Studies (GWAS) enable researchers to identify genetic variants linked to specific traits or diseases by analyzing large-scale genomic datasets.

Combining GATK and GWAS allows for high-precision variant detection and statistical association analysis, helping uncover the genetic basis of complex diseases, drug responses, and population genetics.

However, challenges like data preprocessing, computational requirements, and population stratification must be carefully managed to ensure accurate results. This approach is essential for researchers in genomics, precision medicine, and evolutionary studies, enabling them to conduct reproducible and high-quality genomic research for medical and scientific advancements.