BEAGLE

Introduction

BEAGLE is a tool for genotype phasing and imputation. It is commonly used in population genetics and GWAS workflows to phase genotypes and to impute missing variants using reference panels.

Requirements

BEAGLE is available as a module on Delta and Illinois Campus Cluster (ICC). Requirements are loaded automatically when the module is called:

module load beagle

Usage

The following SLURM batch script can be used as a template for running BEAGLE for basic phasing or imputation:

# Path to Working Directory

myWorkDir="/path/to/my/working/directory"
cd $myWorkDir

## -- Input VCF file (required)
## -- Reference panel VCF file (optional, for imputation)
## -- Output prefix (required)

# Run BEAGLE (basic example)

beagle \
  gt=input.vcf.gz \
  out=beagle_output \
  nthreads=4

References

Browning B. L., Browning S. R. (2021). Genotype Imputation with Millions of Reference Samples. American Journal of Human Genetics, 108(10), 2067–2080.