2 Setup Details

2.1 Requirements

PopTop requires the following modules/programs to be installed:

• Nextflow (20.01.0)
• R (4.1)
• Perl (5.24.4)
• Htslib(1.13)
• Bcftools (1.2)
• Plink(1.90b6.6)
• shapeit (v2.r904) - available from its download site

2.1.1 Local run

The pipeline can also be run locally on a machine with at least 40GB RAM. In this case all the programs mentioned above should be available in any of the current shell $PATH directories.

All requirements (except shapeit) can be installed as modules on JHPCE.