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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.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      The H3A\n                      <jats:sc>GWAS<\/jats:sc>\n                      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.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>The workflow is scalable\u2014laptop to cluster to cloud (e.g., SLURM, AWS Batch, Azure). All required software is containerised and can run under Docker or Singularity.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12859-022-05034-w","type":"journal-article","created":{"date-parts":[[2022,11,19]],"date-time":"2022-11-19T02:03:09Z","timestamp":1668823389000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":13,"title":["H3AGWAS: a portable workflow for genome wide association studies"],"prefix":"10.1186","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0197-2648","authenticated-orcid":false,"given":"Jean-Tristan","family":"Brandenburg","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lindsay","family":"Clark","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gerrit","family":"Botha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sumir","family":"Panji","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shakuntala","family":"Baichoo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Christopher","family":"Fields","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Scott","family":"Hazelhurst","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,11,19]]},"reference":[{"issue":"1","key":"5034_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s43586-021-00056-9","volume":"1","author":"E Uffelmann","year":"2021","unstructured":"Uffelmann E, Huang QQ, Munung NS, de Vries J, Okada Y, Martin AR, et al. 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J Open Source Softw. 2021;6(59):2957. https:\/\/doi.org\/10.21105\/joss.02957.","journal-title":"J Open Source Softw"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-022-05034-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s12859-022-05034-w\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-022-05034-w.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,21]],"date-time":"2022-11-21T03:03:31Z","timestamp":1668999811000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-022-05034-w"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,19]]},"references-count":54,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,12]]}},"alternative-id":["5034"],"URL":"https:\/\/doi.org\/10.1186\/s12859-022-05034-w","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/2022.05.02.490206","asserted-by":"object"}]},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,19]]},"assertion":[{"value":"1 May 2022","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 November 2022","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 November 2022","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declaration"}},{"value":"We have used the AWI-Gen data set as our main example as a real data set. The AWI-Gen study received approval from the Human Research Ethics Committee (Medical), University of the Witwatersrand, South Africa (M121029, M1706110).","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"There is no conflict of interest.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"There is no conflict of interest.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"498"}}