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).
Dalapicolla et al. (2023)
RStudio version
R version
01.Inputs:
vcfs:
metadata:
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Filtering:
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Genetic Structure: PCA | sNMF | DPAC | TESS3
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Genetic Diversity: Ht | Ho | FIS | SNV | pi
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Genetic Distance: FST | Shared Alleles | Relatedness | Kinship | PCAdistance
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Isolation-by-Distance: Mantel Tests | Procrustes
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Fine-Scale Spatial Strucuture: Correlogram | sPCA
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Connectivity: PopGraphs ! EMMS