SSBR-JWAS-Implementation

For genomic estimated breeding value(EBV) and Genome wide association studies(GWAS) using JWAS and XSim. The workflow includes

1. Simulating SNP data using XSim. Files generated: pedigree.txt, phenotype.txt, genotype.txt, map.txt and ID.txt
   
2. Statistical Analysis for EBV and GWAS using JWAS
   
3. Includes XSimPreProcess package for automating XSim -> JWAS analysis.
   
4. To use GWAS function for WPPA in JWAS package run Pkg.add(PackageSpec(name=“JWAS”, rev=“master”)) and then import JWAS.misc by using JWAS.misc
5. Test-Split.jl splits your input files into training and testing sets for Single Step Analysis on JWAS

Steps for adding XSimPreProcess Module for XSim package.

1. push!(LOAD_PATH, "/Path/To/My/Module/") to add XSimPreProcess Module to julia. Requires this push for module use everytime julia is reopned
2. Copy/paste the command in the file ~/.julia/config/startup.jl will extend LOAD_PATH on every Julia startup.

Jupyter-Examples.

Usage of XSimPreProcess module for SSBR-analysis in this folder

Updated Commandline Implementation

ARGS = 5

ARG[1] = Input Genotype Path ARG[2] = Processed Data Path ARG[3] = Analysis Data Path ARG[4] = Number of QTL to set for analysis ARG[5] = Number of Markers to include for Phenotype Simulation

1. Make 3 Directories - 1 for input data, 1 for processed data, 1 for analysis
2. Files inside Input Data - Genotype file, XSim-Map-File
3. Files inside Processed Data - Processed genotype, phenotype, pedigree, mapfile, rowIDs and other files as per pre-processing script
4. Files inside Analysis Data - Output files of JWAS run
5. Run command as follows julia Phenotype-SSBR-Simulation.jl .\Directory1// .\Directory2// .\Directory3// 5 1