PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies.

ABSTRACT: Genome-wide association studies (GWAS) are increasingly being applied to investigate the genetic basis of bacterial traits. However, approaches to perform power calculations for bacterial GWAS are limited. Here we implemented two alternative approaches to conduct power calculations using existing collections of bacterial genomes. First, a sub-sampling approach was undertaken to reduce the allele frequency and effect size of a known and detectable genotype-phenotype relationship by modifying phenotype labels. Second, a phenotype-simulation approach was conducted to simulate phenotypes from existing genetic variants. We implemented both approaches into a computational pipeline (PowerBacGWAS) that supports power calculations for burden testing, pan-genome and variant GWAS; and applied it to c

SUBMITTER: Coll F 

PROVIDER: S-EPMC8956664 | biostudies-literature | 2022 Mar

REPOSITORIES: biostudies-literature