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Bioinformatics. 2016 Dec 1;32(23):3661-3663. Epub 2016 Aug 6.

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

Author information

1
Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montreal Heart Institute Research Center, Montréal, Canada H1T 1C8.
2
Department of Biochemistry and molecular medicine, Université de Montréal, Montreal, Canada H3T 1J4.
3
Department of Medicine, Université de Montréal, Montreal, Canada H3T 1J4.

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.

PMID:
27497439
PMCID:
PMC5181529
DOI:
10.1093/bioinformatics/btw487
[Indexed for MEDLINE]
Free PMC Article

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