myleslab/ripening_time_wgs

WGS project: GWAS for ripening time

Ripening_time_WGS

WGS project: GWAS for ripening time

This repository will contain all the of the R scripts written by Thomas Davies for the WGS Ripening Time Project. For more information, contact Tommy Davies at [email protected].

TABLE OF CONTENTS:

CIRSPR_sites_in_gwas_peak_20231220.R This script calculates and visualizes the number of CRISPR editing sights within the Chromosome 3 signal region identified in chapter 4.

GATK-pipeline-stats-analysis_20231220.R This script calculates and visualizes various metrics collected during variant calling using the GATK workflow, including read pair count and read depth across samples.

LD_plotting_20231220.R This script calculates and visualizes LD for 17 SNPs shared by the WGS and GBS samples.

WGS-GWAS-manhattan-qq-plotter_20231220.R This script plots WGS GWAS results data in the form of a manhattan plot (entire genome) and a QQ plot.

auto_run_gwas_20231220.R This script executes the PRELIMINARY GWAS via the Beluga server.

harv_date_manhattan_plot_zoom_plotter.R This script plots the manhattan plots, many of which are zoom-in plots, for the ripening time WGS GWAS.

harv_date_norm_rd_full_genome_manhattan_20231220.R This script plots the correlation results from the normalized 100bp windows in the form of a manhattan plot.

prelim_gwas_file_formatting_20231220.R This script formats various phenotype and genotype files to make them suitable for the PRELIMINARY GWAS.

rd_win_calc_fast_20231220.R This script calculates the normalized mean read depth from 100bp windows across the genome.

read_depth_100bp_win_correlation_calculator_20231220.R This script runs the correlations between each of the normalized 100bp window means and the ripening time phenotype data.

read_depth_corr_plotter_20231220.R This script examines a few notable correlations from the read depth correlation analysis, and visualizes them.

stacked_plots_20231220.R This script takes data from the GWAS analysis, the normalized read depth analysis, and the Chapter 3 read depth analysis, and plots them together to make a figure.

sv_collector_script_20231220.R This script visualizes the results generated by SV-collector.