1 Quick Start

PopTop is an pipeline preparing genotype data for the in A brief guide to setting up PopTop can be found here. A more detailed and thorough guide is here.

1.1 Setup

1. Clone the PopTop repository with git clone git@github.com:LieberInstitute/PopTop
2. Change directory into the repository with cd PopTop
3. We have made an Rscript to for first time users. This script will serve to install all R packages associated with the pipeline. (TODO)

1.2 Configuration

Right now PopTop is only configured to be run on the JHPCE. Here you will use run_pipeline.sh. Options included in the main script should be modified as appropriate for the experiment. The main script should be submitted as a job (i.e. using qsub). For example: qsub run_pipeline.sh

1.3 Default Parameters

Minimum cutoff minor allele frequency used to filter (‘–maf’ option) maf_min = 0.005

Maximum missing call frequency used to filter (‘–geno’ option) max_missing = 0.05

Minimum Hardy-Weinberg equilibrium exact test p-value threshold (‘–hwe’ option) hwe_min = 0.00001

Value for the ‘–indep-pairwise’ argument to plink indep_pairwise = "50 5 0.2" ### Your config file ###

Find your config file under PopTop/conf/jhpce.config Currently this pipeline is only supported on JHPCE, but we may add more configuration file in the future.