I have two different genotyped data sets - say A and B( Two very different populations). I have done PCA on A and it shows population clusters within the data without any pruning. Pruning removes most of the SNPs.
For the second part, I have to merge A and B and do a PCA on the merged data- this does not show any clusters without pruning. There was not much difference with pruning either.
Thirdly, I tried doing a PCA only on data set B and this also doesn't show population clusters with or without pruning. But from my phenotype data, I know that there is variation.
I did PCA using bfiles in Plink using the --pca flag.
Any suggestions please?