README.md

Snakemake Imputation Workflow For Chip Array Data

Usage

Make sure you have all dependencies solved. Also, make sure all data are using the same reference coordinate, especially paying attention to the chromosome names. All inputs are configured by config/config.yaml. Check config/README for details.

Dependencies

• shapeit2
• impute2
• bcftools
• plink(1.9)
• vcf_addDS
• pandas (python)
• awk (linux)