5 Annotation

• HRC-1000G-check-bim-v4.2.13-NoReadKey is used to align the snps with the HRC in with a submitted job in the flipit.sh step of the pipeline. This file can be downloaded here https://www.well.ox.ac.uk/~wrayner/tools/ However, it is already found in the PopTop github repo and will be downloaded if this repo is cloned.