Vcf2gwas: Python API for comprehensive GWAS analysis using GEMMA.

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

SUBMITTER: Vogt F 

PROVIDER: S-EPMC8756188 | biostudies-literature | 2022 Jan

REPOSITORIES: biostudies-literature