Gimpute: an efficient genetic data imputation pipeline.

Genome Genome-Wide Association Study Genotype Haplotypes Software

Journal

Bioinformatics (Oxford, England)
ISSN: 1367-4811
Titre abrégé: Bioinformatics
Pays: England
ID NLM: 9808944

Informations de publication

Date de publication:
15 04 2019
Historique:
received: 20 02 2018
revised: 09 08 2018
accepted: 18 09 2018
pubmed: 22 9 2018
medline: 19 2 2020
entrez: 22 9 2018
Statut: ppublish

Résumé

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. 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. The Gimpute package is an open source R package and is freely available at https://github.com/transbioZI/Gimpute. Supplementary data are available at Bioinformatics online.

Identifiants

DOI: 10.1093/bioinformatics/bty814 PMID: 30239591
pubmed: 30239591
pii: 5102867
doi: 10.1093/bioinformatics/bty814
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1433-1435

Informations de copyright

© The Author(s) 2018. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Auteurs

Junfang Chen (J)

Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany.

Dietmar Lippold (D)

Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany.

Josef Frank (J)

Department of Genetic Epidemiology in Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.

William Rayner (W)

Radcliffe Department of Medicine, Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Headington, Oxford, UK.
Nuffield Department of Medicine, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, UK.

Andreas Meyer-Lindenberg (A)

Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany.

Emanuel Schwarz (E)

Department of Psychiatry and Psychotherapy, Heidelberg University, Mannheim, Germany.

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Classifications MeSH

questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Génome › Gimpute: an efficient genetic data imputation pipeline.
questionsmedicales.fr › Environnement et santé publique › Santé publique › Méthodes épidémiologiques › Épidémiologie moléculaire › Étude d'association pangénomique › Gimpute: an efficient genetic data imputation pipeline.
questionsmedicales.fr › Phénomènes génétiques › Génotype › Gimpute: an efficient genetic data imputation pipeline.
questionsmedicales.fr › Phénomènes génétiques › Génotype › Haplotypes › Gimpute: an efficient genetic data imputation pipeline.
questionsmedicales.fr › Sciences de l'information › Méthodologies informatiques › Logiciel › Gimpute: an efficient genetic data imputation pipeline.