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.
The easiest and recommended way to install and run PowerBacGWAS is via its Docker/Nextflow implementation.
You will need to:
- Install Docker or Singularity
- Install Nextflow
- Download PowerBacGWAS Nextflow files from GitHub:
git clone https://github.com/francesccoll/powerbacgwas/
cd powerbacgwas/nextflow
nextflow run main.nf --helpSee the PowerBacGWAS wiki page for examples of Nextflow commands.
PowerBacGWAS consists of a set of Python and R scripts that would work provided that all required dependencies below (both python modules and software) are installed in your local machine.
- Python3 version >= 3.6.9
- R version >= 3.6.3
- PastML version >= 1.9.20
- plink version >= PLINK v1.90b6.17 64-bit (28 Apr 2020)
- GCTA version >= version 1.93.2
- pyseer version >= pyseer 1.3.7-dev
- bcftools version >= 1.9
- bgzip version >= 1.9
- tabix version >= 1.9
- cyvcf2 version >= 0.20.8
- scipy version >= 1.5.4
- numpy version >= 1.19.4
- pandas version >= 1.1.4
- PyVCF version >= 0.6.8
- optparse >= 1.6.6
- ggplot2 version >= 3.3.1
Download the latest release from this github repository or clone it.
git clone https://github.com/francesccoll/powerbacgwas/cd powerbacgwas/As the pipeline uses scripts from PastML and PySeer, clone their GitHub directories into the downloaded powerbacgwas folder:
git clone https://github.com/evolbioinfo/pastmlgit clone https://github.com/mgalardini/pyseerPlease read the PowerBacGWAS wiki page for full usage instructions and tutorials.
PowerBacGWAS is a free software, licensed under GNU General Public License v3.0
Use the issues page to report on installation and usage issues.
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