I would like to perform principal component analysis on a pool-seq SNP dataset. I've been looking into methods for doing this, but have had trouble finding examples that may apply for pooled data as opposed to individual genotypes. For example, I'm not sure if PLINK can be used to run PCA on pooled datasets. Is anyone familiar with whether PLINK can be used for PCA on pooled SNP data, and, if not, any toolkit or approach that would be ideal to use for PCA on pooled data?
Thanks in advance!