Junfang Chen1, Dietmar Lippold1, Josef Frank2, William Rayner3,4,5, Andreas Meyer-Lindenberg1, Emanuel Schwarz1. 1. Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany. 2. Department of Genetic Epidemiology in Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany. 3. Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Headington, Oxford, UK. 4. Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. 5. Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.
Abstract
MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: The Gimpute package is an open source R package and is freely available at https://github.com/transbioZI/Gimpute. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
MOTIVATION: 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. RESULTS: 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. AVAILABILITY AND IMPLEMENTATION: The Gimpute package is an open source R package and is freely available at https://github.com/transbioZI/Gimpute. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Authors: Jon Foss-Skiftesvik; Christian Munch Hagen; René Mathiasen; Dea Adamsen; Marie Bækvad-Hansen; Anders D Børglum; Merete Nordentoft; Thomas Werge; Michael Christiansen; Kjeld Schmiegelow; Marianne Juhler; Preben Bo Mortensen; David Michael Hougaard; Jonas Bybjerg-Grauholm Journal: Childs Nerv Syst Date: 2020-11-23 Impact factor: 1.475