README.md

Repository for scripts and other data analysis protocols for Aegilops tauschii diversity project.

This paper has been published and can be found here https://www.frontiersin.org/articles/10.3389/fpls.2019.00009/full

1. Run Tassel5 GBSv2 pipeline using the provided keyfile in SNP_calling_scripts folder to call SNPs.

2. required_files contain files with some required metadata.

3. Use the R scripts to perform a specific analysis.

   • 1.File.formatting.R - format hapfile for further analyses
   • 2.SNP.Filtering.R - filter SNPs based on criteria given in the paper
   • 3.PCA_Cluster.R - plot PCA plots, biplots, and violin plots
   • 4.Genetic.diversity.R - compute genetic diversity statistics
   • 5_Hybrid_graphical.R - plot hybrids graphically