GWAS notebook

Getting Started

In this notebook, a collection of population genetic data analysis codes has been compiled to be a tool for development and comprehensive analysis One of the advantages of this notebook is that we can develop and change the edited codes at any time in order to have the best pipeline of this complete one for doing the GWAS prrojects..

Provision and preparation of data

    -- Prepare the raw genotype files 

Installation

A step by step pipeline for download and installing GWAS software and tools

#Step_1 Downloading & installation toools

Plink

Plink tools can be download from Plink)

PLINK1.9 : https://www.cog-genomics.org/plink/
PLINK2 : https://www.cog-genomics.org/plink/2.0/

#Create directories
cd ~
mkdir tools
cd tools
mkdir bin
mkdir plink
mkdir plink2

Style test

Checks if the best practices and the right coding style has been used.

Give an example