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. 2022 Nov 19;23(1):498.
doi: 10.1186/s12859-022-05034-w.

H3AGWAS: a portable workflow for genome wide association studies

Jean-Tristan Brandenburg  1 , Lindsay Clark  2   3 , Gerrit Botha  4 , Sumir Panji  4 , Shakuntala Baichoo  5 , Christopher Fields  2 , Scott Hazelhurst  6   7
Affiliations

H3AGWAS: a portable workflow for genome wide association studies

Jean-Tristan Brandenburg et al. BMC Bioinformatics. .

Abstract

Background: Genome-wide association studies (GWAS) are a powerful method to detect associations between variants and phenotypes. A GWAS requires several complex computations with large data sets, and many steps may need to be repeated with varying parameters. Manual running of these analyses can be tedious, error-prone and hard to reproduce.

Results: The H3AGWAS workflow from the Pan-African Bioinformatics Network for H3Africa is a powerful, scalable and portable workflow implementing pre-association analysis, implementation of various association testing methods and post-association analysis of results.

Conclusions: The workflow is scalable-laptop to cluster to cloud (e.g., SLURM, AWS Batch, Azure). All required software is containerised and can run under Docker or Singularity.

Keywords: Association testing; Docker; Genome-wide association study; Nextflow; Pipeline; Post-association analysis; Quality control; Singularity; Workflow.

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Conflict of interest statement

There is no conflict of interest.

There is no conflict of interest.

Figures

Fig. 1
Fig. 1
Overview of GWA studies from DNA sample until post-association analysis, box in blue corresponding to part of GWA studies present in H3AGWAS workflow and text in red corresponding to scripts in H3AGWAS workflow
Fig. 2
Fig. 2
Workflow of association testing each background color represent different steps from input to output with preparation of input data, generated relatedness matrix or GRM to take account population structure and association testing
See this image and copyright information in PMC

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