Admixture example

Admixture is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets (publication; website).

#(On TACC)
#navigate to directory
cd intro_to_rad_2018/admixture
  
#convert the VCF file into .ped file for input into Admixture
plink2 --vcf corals.vcf --make-bed --out corals --allow-extra-chr
  
#Run Admixture on the .ped file made by PLINK specifying an expectation of three ancestral populations
admixture corals.bed 3
  
#move the file corals.3.Q to your computer and use plot_admixture.R to plot the results
#Contrast the results with PCA plotted from the same data (PCA exercise)