Hi Emma, you could do something like this, yes. The question would be, how you determined your variants. If they are in VCF format, you could use something like glactools (https://github.com/grenaud/glactools) to generate the required formats to e.g. perform a PCA on your datasets.

That might already give you a broad overview on your dataset and is a commonly performed type of analysis in population genetics. As you don't really have a large panel of individuals to compare to, you might see some spurious samples falling outside of other individuals, but thats simply a problem of having too few individuals and/or variants to look at.