{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,26]],"date-time":"2026-02-26T20:34:11Z","timestamp":1772138051802,"version":"3.50.1"},"reference-count":11,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2022,4,20]],"date-time":"2022-04-20T00:00:00Z","timestamp":1650412800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"name":"NHLBI BioData Catalyst ecosystem. This work was supported by the National Institutes of Health funding sources","award":["1OT3 HL147154-01"],"award-info":[{"award-number":["1OT3 HL147154-01"]}]},{"name":"NHLBI BioData Catalyst ecosystem. This work was supported by the National Institutes of Health funding sources","award":["5116786"],"award-info":[{"award-number":["5116786"]}]},{"name":"NHLBI BioData Catalyst ecosystem. This work was supported by the National Institutes of Health funding sources","award":["K99-HL151877"],"award-info":[{"award-number":["K99-HL151877"]}]},{"name":"NHLBI BioData Catalyst ecosystem. This work was supported by the National Institutes of Health funding sources","award":["R35-CA197449"],"award-info":[{"award-number":["R35-CA197449"]}]},{"name":"NHLBI BioData Catalyst ecosystem. This work was supported by the National Institutes of Health funding sources","award":["U01-HG009088"],"award-info":[{"award-number":["U01-HG009088"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,5,26]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Summary<\/jats:title>\n                    <jats:p>We developed the variant-Set Test for Association using Annotation infoRmation (STAAR) workflow description language (WDL) workflow to facilitate the analysis of rare variants in whole genome sequencing association studies. The open-access STAAR workflow written in the WDL allows a user to perform rare variant testing for both gene-centric and genetic region approaches, enabling genome-wide, candidate and conditional analyses. It incorporates functional annotations into the workflow as introduced in the STAAR method in order to boost the rare variant analysis power. This tool was specifically developed and optimized to be implemented on cloud-based platforms such as BioData Catalyst Powered by Terra. It provides easy-to-use functionality for rare variant analysis that can be incorporated into an exhaustive whole genome sequencing analysis pipeline.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The workflow is freely available from https:\/\/dockstore.org\/workflows\/github.com\/sheilagaynor\/STAAR_workflow.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac272","type":"journal-article","created":{"date-parts":[[2022,4,15]],"date-time":"2022-04-15T07:12:02Z","timestamp":1650006722000},"page":"3116-3117","source":"Crossref","is-referenced-by-count":12,"title":["STAAR workflow: a cloud-based workflow for scalable and reproducible rare variant analysis"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7869-5223","authenticated-orcid":false,"given":"Sheila M","family":"Gaynor","sequence":"first","affiliation":[{"name":"Department of Biostatistics, Harvard TH Chan School of Public Health , Boston, MA 02115, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7619-1868","authenticated-orcid":false,"given":"Kenneth E","family":"Westerman","sequence":"additional","affiliation":[{"name":"Department of Medicine, Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA 02114, USA"},{"name":"Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"},{"name":"Department of Medicine, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"Lea L","family":"Ackovic","sequence":"additional","affiliation":[{"name":"Seven Bridges , Charlestown, MA 02129, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8151-0106","authenticated-orcid":false,"given":"Xihao","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard TH Chan School of Public Health , Boston, MA 02115, USA"}]},{"given":"Zilin","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard TH Chan School of Public Health , Boston, MA 02115, USA"}]},{"given":"Alisa K","family":"Manning","sequence":"additional","affiliation":[{"name":"Department of Medicine, Clinical and Translational Epidemiology Unit, Mongan Institute, Massachusetts General Hospital, Boston, MA 02114, USA"},{"name":"Metabolism Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA"},{"name":"Department of Medicine, Harvard Medical School, Boston, MA 02115, USA"}]},{"given":"Anthony","family":"Philippakis","sequence":"additional","affiliation":[{"name":"The Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7067-7752","authenticated-orcid":false,"given":"Xihong","family":"Lin","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Harvard TH Chan School of Public Health , Boston, MA 02115, USA"},{"name":"The Broad Institute of MIT and Harvard, Cambridge, MA 02124, USA"},{"name":"Department of Statistics, Harvard University, Cambridge, MA 02138, USA"}]}],"member":"286","published-online":{"date-parts":[[2022,4,20]]},"reference":[{"key":"2023041403080536900_","year":"2020"},{"key":"2023041403080536900_","doi-asserted-by":"crossref","first-page":"260","DOI":"10.1016\/j.ajhg.2018.12.012","article-title":"Efficient variant set mixed model association tests for continuous and binary traits in large-scale whole-genome sequencing studies","volume":"104","author":"Chen","year":"2019","journal-title":"Am. 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