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GWAS Pipeline for H3Africa

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posted on 11.05.2021, 16:09 authored by Scott Hazelhurst, Jean-Tristan Brandenburg, Sumir PanjiSumir Panji
H3Agwas is a simple human GWAS analysis workflow for data quality control (QC) and basic association testing developed by H3ABioNet. It is an extension of the witsGWAS pipeline for human genome-wide association studies built at the Sydney Brenner Institute for Molecular Bioscience. H3Agwas uses Nextflow as the basis for workflow management and has been dockerised to facilitate portability.

The original version of the H3Agwas was published in June 2017 with minor updates and bug fixes through the rest of the year. Based on experience with large data sets, the pipelines were considerably revised with additional features, reporting and a slightly different workflow.



H3ABioNet, Faculty of Health Sciences, University of Cape Town