Developers from H3ABioNet developed a genome-wide association study (GWAS) analysis pipeline for data quality control (QC) and basic association testing, which can be found on Github here. The pipeline uses Nextflow as the basis for workflow management and has been containerised using Docker to facilitate portability (Singularity containerisation, which is necessary to run on UCT's high performance cluster, has not been tested fully). The overall development of the pipeline was driven by the Wits University team under guidance of Scott Hazelhurst. The pipeline has been tested extensively on the Wits high performance cluster but if you need assistance in getting it up and running somewhere else please contact the BST team.
H3AbioNet has also developed a chip imputation pipeline that is specifically aimed at imputing missing genome data from the Illumina H3Africa genotype array (it will however work with other Illumina chips as well). The pipeline can be accessed here and has been tested on UCT's hex and CBIO clusters. If you however need to get it up and running somewhere else please contact the BST team.