Can I build a phylgenetic tree using SNPs obtained by differen techniques?

Question

[rimgubaev]

I had GBS libraries for several plant lines then I performed SNP calling using GATK pipeline. So my question is the following: is it appropriate to compare obtained SNPs with SNPs obtained in other studies by arrays or RAD-seq for example? Namely I want to build a phylogenetic tree and see how my plant lines relate to the already published.