PCA on pooled and single individuals

Hello all,

I am trying to carry out a population structure analysis using a set of samples that includes pooled and single individuals. After performing the PCA using SNPRelate, pooled individuals are clustered together, which suggests that the sample type is an averaging effect going on in the pooled samples.

Does anyone know a reliable method to do PCA on a mix of pooled and non pooled individuals?

Thanks in advance!