Molgenis-impute

MOLGENIS-impute is an automated software tool that streamlines the entire genotype imputation process. It makes it easier for researchers to perform high-quality imputation without requiring extensive expertise in setting up and running complex pipelines. The tool automates all the necessary steps, including genome build liftover, genotype phasing using SHAPEIT2, quality control, sample, chromosomal chunking/merging, and imputation using IMPUTE2.

One of the critical features of MOLGENIS-impute is its ability to scale out imputation tasks in parallel on various computing environments, such as local servers, cloud servers, clusters, and grids. It is particularly useful for large genotype datasets that require significant computational resources.

The tool is built on the MOLGENIS-compute platform, simplifying pipeline management and submitting bioinformatics tasks in High-Performance Computing (HPC) environments. MOLGENIS-impute has been tested by researchers with diverse backgrounds and expertise, successfully imputing over 30,000 samples using the 1,000 Genomes Project and the Genome of the Netherlands data as reference panels.

MOLGENIS-impute prioritizes ease of use, requiring minimal dependencies and providing a simple command-line interface. It allows researchers to apply best practices in imputation without extensive knowledge of workflow systems or programming. The tool is customizable and can be integrated into other bioinformatics pipelines.