Material for Master Course MER2024
Load an interactive mode in Arina cluster
interactive -n 4 -p vfast -r mer3
Load necesary modules
module load BCFtools/1.15.1-GCC-11.3.0
module load Python/3.10.4-GCCcore-11.3.0
a) Conduct a PCA from of unlinked SNPs from 50 anchovy specimens
Compute a covariance matrix with PCAngsd (https://github.com/Rosemeis/pcangsd)
./pcangsd_hwe.sh Anchovy_data Anchovy_PCA 4
b) Estimate Admixture proportions with NGSAdmix (http://www.popgen.dk/software/index.php/NgsAdmix)
screen -S NGSadmix
./ngsadmix.sh Anchovy_data Anchovy_Admixture 2 10 4 1>./Anchovy_Admixture/ngsadmix.err 2>./Anchovy_Admixture/ngsadmix.log