MOLGENIS compute

MOLGENIS compute orchestrates pipeline execution and resource management to automate genotype imputation workflows and large-scale bioinformatics tasks for GWAS, meta-analyses, and fine mapping.

Key Features:

• Pipeline Management: Submits and monitors bioinformatics tasks across local servers, cloud virtual machines (VMs), PBS/SGE clusters, and grid environments.
• Integration with Imputation Tools: Integrates with MOLGENIS-impute to automate genotype imputation processes for genome-wide association studies (GWAS), meta-analyses, and fine mapping.
• Automated Setup and Execution: Automates download and installation of required tools, reference data, and scripts to set up and execute pipelines.
• Scalability and Flexibility: Processes large genotype datasets via parallel computing and supports customization by integrating additional computational steps.
• Broad Testing and Validation: Validated in HPC environments including PBS/SGE clusters, cloud VMs, and grid setups, and used to impute over 30,000 samples with reference datasets such as the 1,000 Genomes Project and Genome of the Netherlands.

Scientific Applications:

• Genome-Wide Association Studies (GWAS): Facilitates genotype imputation to increase variant density and power in association analyses.
• Meta-Analyses: Enables harmonized imputation across studies to support combined analyses.
• Fine Mapping: Supports high-resolution localization of causal variants through imputation.

Methodology:

Automates genome build liftover, genotype phasing using SHAPEIT2, quality control, and imputation with IMPUTE2, and optimizes performance via sample and chromosomal chunking/merging in parallel computing environments.