We will go through a simple and more complex example on how to use PCAngsd with visualization of the data.

PCA with admixture aware priors

This example will perform a PCA analysis on 1000 genotype likelihoods.

Every time you open a new terminal window, set the paths to the program and the input file.

PCAngsd=~/Software/PCAngsd

Test the link

ls $PCAngsd

Download and Set the path to the input file, for example:

*ANDERS*

cd wget popgen.dk/software/download/NGSadmix/data/input.gz maybe change it to:

wget popgen.dk/software/download/PCAngsd/data/input.gz

GL1000Genomes=./input.gz

*ANDERS*

PCAngsdTutorial