Population Genomics Pipeline using SNPs data in VCF files from Reduced-representation sequencing (RRS), such as, Genotype-by-Sequencing (GBS) and Restriction-site Associated DNA Sequencing (RAD-Seq).
Software used in this pipeline:
RStudio version 2022.02.3 Build 492
Inputs: .vcf files, reference file for Dioclea dataset, and .csv files with geographical coordinates for both datasets
Filtering: R scripts for filtering neutral SNPs.
Genetic Structure: R scripts for basic genomic structure analyses PCA | sNMF | DPAC | TESS3
Genetic Diversity and Distance: R scripts for basic genomic diversity Ht | Ho | FIS | FST