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Molgenis-impute: imputation pipeline in a box.
Alexandros Kanterakis1, Patrick Deelen2, Freerk van Dijk3
1Department of Genetics, Genomics Coordination Center, University Medical Center Groningen and University of Groningen, Genetics, UMCG, PO Box 30 001, 9700 RB, Groningen, The Netherlands. alexandros.kanterakis@gmail.com.
MOLGENIS-impute simplifies genotype imputation for genomic studies by automating complex pipelines. This "imputation in a box" solution requires minimal expertise, making best-practice imputation accessible to more researchers.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- Genotype imputation is crucial for genomic analyses like GWAS, meta-analyses, and fine mapping.
- Setting up imputation pipelines requires significant expertise and computational resources, especially for large datasets.
Purpose of the Study:
- To present MOLGENIS-impute, an automated solution for genotype imputation.
- To simplify the setup and execution of imputation pipelines for researchers.
Main Methods:
- MOLGENIS-impute automates genome build liftover, genotype phasing (SHAPEIT2), quality control, and imputation (IMPUTE2).
- It utilizes the MOLGENIS-compute platform for managing bioinformatics tasks in High Performance Computing (HPC) environments.
- All necessary tools, data, and scripts are installed in a single step.
Main Results:
- MOLGENIS-impute successfully automated imputation processes for over 30,000 samples.
- Tested across diverse HPC environments including clusters, cloud VMs, and grids.
- Demonstrated ease of use for researchers with varying technical backgrounds.
Conclusions:
- MOLGENIS-impute prioritizes ease of use, configuration, and execution of imputation.
- It offers a simple command-line interface with minimal dependencies, preserving flexibility.
- The open-source tool is built on MOLGENIS-compute, allowing customization and integration into other pipelines.
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