prewas

prewas processes bacterial variant data in R to generate binary SNP and gene matrices that improve data pre-processing for bacterial genome-wide association studies (bGWAS).

Key Features:

• Binary SNP Matrix Creation: Transforms whole-genome alignments into a binary single nucleotide polymorphism (SNP) matrix.
• Multiallelic Site Representation: Supports multiple-line representations for multiallelic sites so that all alleles are represented.
• Overlapping Genes Handling: Provides multi-line representation for SNPs located within overlapping genes to attribute variants to each gene.
• Reference Allele Selection: Allows selection of reference alleles to ensure consistent comparisons across datasets.
• Gene Matrix Output: Collapses SNPs into genes to produce a binary gene matrix for gene-based bGWAS.
• Reproducibility and Interpretability: Standardizes preprocessing of multiallelic sites, overlapping genes, and reference alleles to avoid masking minor alleles and improve reproducibility and interpretability.

Scientific Applications:

• Bacterial genome-wide association studies (bGWAS): Enhances variant representation to maximize information used in association testing for microbial phenotypes.
• Gene-based association analysis: Produces binary gene matrices that support gene-level association testing and evolutionary interpretability.

Methodology:

Implements standardized preprocessing for multiallelic sites and overlapping genes, uses multi-line variant representations, and outputs binary SNP-based and gene-based matrices.