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RICOPILI, an open-sourced Perl-based pipeline was developed to address the challenges of rapidly processing large-scale multi-cohort GWAS studies including quality control (QC), imputation and downstream analyses. The pipeline is computationally efficient with portability to a wide range of high-performance computing environments. RICOPILI was created as the Psychiatric Genomics Consortium pipeline for GWAS and adopted by other users. The pipeline features (i) technical and genomic QC in case-control and trio cohorts, (ii) genome-wide phasing and imputation, (iv) association analysis, (v) meta-analysis, (vi) polygenic risk scoring and (vii) replication analysis. Notably, a major differentiator from other GWAS pipelines, RICOPILI leverages on automated parallelization and cluster job management approaches for rapid production of imputed genome-wide data. A comprehensive meta-analysis of simulated GWAS data has been incorporated demonstrating each step of the pipeline. This includes all the associated visualization plots, to allow ease of data interpretation and manuscript preparation. Simulated GWAS datasets are also packaged with the pipeline for user training tutorials and developer work.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>RICOPILI has a flexible architecture to allow for ongoing development and incorporation of newer available algorithms and is adaptable to various HPC environments (QSUB, BSUB, SLURM and others). Specific links for genomic resources are either directly provided in this paper or via tutorials and external links. The central location hosting scripts and tutorials is found at this URL: https:\/\/sites.google.com\/a\/broadinstitute.org\/RICOPILI\/home<\/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\/btz633","type":"journal-article","created":{"date-parts":[[2019,8,7]],"date-time":"2019-08-07T15:14:03Z","timestamp":1565190843000},"page":"930-933","source":"Crossref","is-referenced-by-count":307,"title":["RICOPILI: Rapid Imputation for COnsortias PIpeLIne"],"prefix":"10.1093","volume":"36","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4256-7844","authenticated-orcid":false,"given":"Max","family":"Lam","sequence":"first","affiliation":[{"name":"Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT , Cambridge, MA 02142, USA"},{"name":"Analytic and Translational Genetics Unit, Massachusetts General Hospital , Cambridge, MA 02114, USA"},{"name":"Division of Psychiatry Research, The Zucker Hillside Hospital, Northwell Health , Glen Oaks, NY 11004, USA"},{"name":"Research Division, Institute of Mental Health Singapore , Singapore 539747, Singapore"},{"name":"Human Genetics, Genome Institute of Singapore , Singapore 138672, Singapore"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Swapnil","family":"Awasthi","sequence":"additional","affiliation":[{"name":"Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT , Cambridge, MA 02142, USA"},{"name":"Department of Psychiatry and Psychotherapy, Charit\u00e9 - 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