{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,5]],"date-time":"2025-11-05T21:00:33Z","timestamp":1762376433223,"version":"3.37.3"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2018,9,19]],"date-time":"2018-09-19T00:00:00Z","timestamp":1537315200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001659","name":"Deutsche Forschungsgemeinschaft","doi-asserted-by":"publisher","award":["SCHW 1768\/1-1"],"award-info":[{"award-number":["SCHW 1768\/1-1"]}],"id":[{"id":"10.13039\/501100001659","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Motivation<\/jats:title><jats:p>Genotype imputation is essential for genome-wide association studies (GWAS) to retrieve information of untyped variants and facilitate comparability across studies. However, there is a lack of automated pipelines that perform all required processing steps prior to and following imputation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Based on widely used and freely available tools, we have developed Gimpute, an automated processing and imputation pipeline for genome-wide association data. Gimpute includes processing steps for genotype liftOver, quality control, population outlier detection, haplotype pre-phasing, imputation, post imputation, data management and the extension to other existing pipeline.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>The Gimpute package is an open source R package and is freely available at https:\/\/github.com\/transbioZI\/Gimpute.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty814","type":"journal-article","created":{"date-parts":[[2018,9,18]],"date-time":"2018-09-18T11:10:18Z","timestamp":1537269018000},"page":"1433-1435","source":"Crossref","is-referenced-by-count":9,"title":["Gimpute: an efficient genetic data imputation pipeline"],"prefix":"10.1093","volume":"35","author":[{"given":"Junfang","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany"}]},{"given":"Dietmar","family":"Lippold","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany"}]},{"given":"Josef","family":"Frank","sequence":"additional","affiliation":[{"name":"Department of Genetic Epidemiology in Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany"}]},{"given":"William","family":"Rayner","sequence":"additional","affiliation":[{"name":"Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Headington, Oxford, UK"},{"name":"Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK"},{"name":"Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK"}]},{"given":"Andreas","family":"Meyer-Lindenberg","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany"}]},{"given":"Emanuel","family":"Schwarz","sequence":"additional","affiliation":[{"name":"Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany"}]}],"member":"286","published-online":{"date-parts":[[2018,9,19]]},"reference":[{"key":"2023012808251893700_bty814-B2","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","article-title":"A global reference for human genetic variation","volume":"526","year":"2015","journal-title":"Nature"},{"key":"2023012808251893700_bty814-B1","doi-asserted-by":"crossref","first-page":"6733","DOI":"10.1038\/s41598-017-06905-6","article-title":"Inclusion of population-specific reference panel from India to the 1000 genomes phase 3 panel improves imputation accuracy","volume":"7","author":"Ahmad","year":"2017","journal-title":"Sci. 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