Dataset Information

Genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.

ABSTRACT: Genotype imputation is now commonly performed following genome-wide genotyping experiments. Imputation increases the density of analyzed genotypes in the dataset, enabling fine-mapping across the genome. However, the process of imputation using the most recent publicly available reference datasets can require considerable computation power and the management of hundreds of large intermediate files. We have developed genipe, a complete genome-wide imputation pipeline which includes automatic reporting, imputed data indexing and management, and a suite of statistical tests for imputed data commonly used in genetic epidemiology (Sequence Kernel Association Test, Cox proportional hazards for survival analysis, and linear mixed models for repeated measurements in longitudinal studies).

Availability and implementation

The genipe package is an open source Python software and is freely available for non-commercial use (CC BY-NC 4.0) at https://github.com/pgxcentre/genipe Documentation and tutorials are available at http://pgxcentre.github.io/genipe CONTACT: louis-philippe.lemieux.perreault@statgen.org or marie-pierre.dube@statgen.orgSupplementary information: Supplementary data are available at Bioinformatics online.

SUBMITTER: Lemieux Perreault LP

PROVIDER: S-EPMC5181529 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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genipe: an automated genome-wide imputation pipeline with automatic reporting and statistical tools.

Lemieux Perreault Louis-Philippe LP Legault Marc-André MA Asselin Géraldine G Dubé Marie-Pierre MP

Bioinformatics (Oxford, England) 20160806 23

Genotype imputation is now commonly performed following genome-wide genotyping experiments. Imputation increases the density of analyzed genotypes in the dataset, enabling fine-mapping across the genome. However, the process of imputation using the most recent publicly available reference datasets can require considerable computation power and the management of hundreds of large intermediate files. We have developed genipe, a complete genome-wide imputation pipeline which includes automatic repo ...[more]

PMID: 27497439

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