Explore SNP filtering thresholds (minor allele filtering and missingness) by estimating population structure and calculating diversity indices. I might just explore the filtering thresholds with PCA and diversity indices and decide on a threshold before moving on to the more involved pop structure analyses.
[x] determine range of filtering thresholds to explore
[x] pi
[x] theta
[ ] conStruct
[x] PCA
[x] dxy
[ ] variational autoencoder- popvae (bonus, if there's time)
Explore SNP filtering thresholds (minor allele filtering and missingness) by estimating population structure and calculating diversity indices. I might just explore the filtering thresholds with PCA and diversity indices and decide on a threshold before moving on to the more involved pop structure analyses.