Getting started

Download Plink v1.9 and place in working directory

You can skip this step if Plink is already installed on your machine and part of your path

i.e., editing your .mybashrc config file in MacOS with emacs

1. emacs ~/.my.bashrc
2. Type in export PATH=$PATH:/PATH/TO/PLINK to new line
3. Control-x Control-s Control-x control-c
4. source ~/.mybashrc to incorporate changes

R needs to be installed to run FLEET

https://cran.r-project.org/mirrors.html (R latest version) https://www.rstudio.com/products/rstudio/download/ (Rstudio)

• Install the following packages if not present in library:

1. plyr
2. foreach and doParallel
3. GenomicRanges
4. ggplot2 and ggrepel
5. data.table

Bedtools needs to be installed and added to $PATH:

http://bedtools.readthedocs.io/en/latest/content/installation.html

Example of running FLEET:

Navigate to FLEET directory or have in $PATH:

export PATH=$PATH:/usr/username/documents/FLEET

gunzip scz2014_full.txt.gz

FLEET.R --gwas scz2014_full.txt --snp-field snipd --clump-field p --out scz2014 --threads 3