<i>vcf2gwas</i> : Python API for comprehensive GWAS analysis using GEMMA
Frank Vogt, Gautam Shirsekar, Detlef Weigel
Abstract
MOTIVATION: Genome-wide association study (GWAS) requires a researcher to perform a multitude of different actions during analysis. From editing and formatting genotype and phenotype information to running the analysis software to summarizing and visualizing the results. A typical GWAS workflow poses a significant challenge of utilizing the command-line, manual text-editing and requiring knowledge of one or more programming/scripting languages, especially for newcomers. RESULTS: vcf2gwas is a package that provides a convenient pipeline to perform all of the steps of a traditional GWAS workflow by reducing it to a single command-line input of a Variant Call Format file and a phenotype data file. In addition, all the required software is installed with the package. vcf2gwas also implements several useful features enhancing the reproducibility of GWAS analysis. AVAILABILITY AND IMPLEMENTATION: The source code of vcf2gwas is available under the GNU General Public License. The package can be easily installed using conda. Installation instructions and a manual including tutorials can be accessed on the package website at https://github.com/frankvogt/vcf2gwas. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.