francesccoll/powerbacgwas

PowerBacGWAS is a computational pipeline to conduct power calculations for bacterial GWAS. It uses existing collections of bacterial genomes to establish the sample sizes required to detect statistical significant associations for a given genotype frequency and effect size (or phenotype heritability). It supports a range of genomic variation including SNPs, indels, and variation in gene content (pan-genome). Here, we make the code available, and provide installation and usage instructions. PowerBacGWAS can be applied to any bacterial population Here we applied it to three different bacterial species: Enterococcus faecium, Klebsiella pneumoniae, and Mycobacterium tuberculosis.

Keywords

Bacterial genomes, Power calculation, Bacterial GWAS, Genome-wide association studies