Admixture

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

Exercise:

This exercise is to be done on your personal computer or on TACC.

There isn't a windows version, so windows users should try it on TACC.

Instructions for doing the exercise on your personal computer:

Download and unzip the exercise files:

exercise_files

Download and unzip PLINK into the exercise directory:

https://www.cog-genomics.org/plink/2.0/

Download and unzip Admixture into the exercise directory:

https://www.genetics.ucla.edu/software/admixture/download.html

Navigate to the exercise directory and execute commands in the code block below:

Run Admixture with Mac

#move the admixture executable into the exercise directory
mv admixture_macosx-1.3.0/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
 
#Plot the results using plot_admixture.R

#Contrast the results with PCA plotted from the same data (PCA exercise)

Instructions for doing the exercise on TACC:

Run Admixture on TACC

#go to scratch
cds
 
#copy over the exercise file
cp /work/02260/grovesd/lonestar/intro_to_rad_2017/admixture_exercise.zip .
 
#unzip it and go to the directory
unzip admixture_exercise.zip
cd admixture_exercise

#download and unzip PLINK
wget http://s3.amazonaws.com/plink2-assets/plink2_linux_x86_64_20171102.zip
unzip plink2_linux_x86_64_20171102.zip
 
#download and unzip Admixture
wget https://www.genetics.ucla.edu/software/admixture/binaries/admixture_linux-1.3.0.tar.gz --no-check-certificate
tar -zxvf admixture_linux-1.3.0.tar.gz
 
#move the admixture executable to the exercise directory
mv admixture_linux-1.3.0/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 files corals.3.Q, plot_admixture.R, and names.txt to your computer and use plot_admixture.R to plot the results
#Contrast the results with PCA plotted from the same data (PCA exercise)