/Choi_etal_O.glaberrima_PopGenome

Primary LanguageRGNU General Public License v3.0GPL-3.0

Scripts and commands used for Choi et al. 2019 Plos Genet Oryza glaberrima population genomics study

https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1007414

All files shown in the script or commands below can be found in dryad: https://datadryad.org/resource/doi:10.5061/dryad.t7g7cj4

commands taken from raw FASTQ to BAM to VCF generation

FromFASTQ_to_VCF.sh

script and commands for calculating and plotting LD

calculate LD

LD_calculator.sh LD_calculator.r

plot LD

plot_LD.r

generate output for plotting genotypes from VCF region of interest

haplotype_view_generate.sh

commands for ploting (visualize) the genotypes

plot_haplotype_view.r

commands for plotting geography of West Africa

plot_WestAfrica_geo.r

plot haplotype network

plot_haplonetwork.r

visualize the NGSadmix results

plot_ngsAdmix.r

visualize NGScovar (PCA) results

plot_ngsCovar.r