This pipeline is designed for imputing and filtering genotyping data using Plink, Beagle, and BCFtools. It includes steps for filtering panels, checking duplicated markers, and imputing missing data.
The following software tools are required to run the pipeline:
#Usage ./imputation_pipeline.sh -p /path/to/plink -r reference_panel -o /path/to/output -i /path/to/input -t target_panel -B /path/to/beagle.jar -b /path/to/bcftools