vcf2gwas

vcf2gwas integrates bcftools, PLINK, and GEMMA to perform genome-wide association studies (GWAS) directly from Variant Call Format (VCF) files to identify genotype–phenotype associations.

Key Features:

• Integration with bcftools, PLINK, and GEMMA: Unifies bcftools, PLINK, and GEMMA into a single workflow for end-to-end GWAS processing.
• VCF-based GWAS: Performs GWAS starting from Variant Call Format (VCF) files and handles required genotype and phenotype data preprocessing and formatting.
• Reproducibility: Provides an integrated workflow that supports reproducible GWAS analyses across datasets.
• Dimensionality Reduction: Includes methods to reduce the dimensionality of phenotypic data for downstream analyses.
• Comparative Variant Analysis: Enables comparison of significant variants with specified genes or genomic regions of interest.
• Post-analysis Summaries and Visualization: Produces summaries and visualizations of GWAS results to support interpretation.

Scientific Applications:

• Association Mapping: Identifying genetic variants associated with complex traits through GWAS.
• Gene–Environment Interaction Analysis: Exploring gene–environment interactions using association results.
• Cross-study Reproducibility: Supporting reproducible analysis workflows for comparisons across studies and datasets.

Methodology:

Leverages bcftools, PLINK, and GEMMA within a unified framework to process VCF genotype data, perform association testing, apply dimensionality reduction to phenotypic data, and generate summary and visualization outputs.