Gimpute: an efficient genetic data imputation pipeline

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.