How to get SNPs (variant calling) from .gff or .align file?

Question

[mthm]

I have masked several genomes each belonging to a separate population to a repeats library and I have got the gff file and the alignment files of the masked regions as outputs (using RepeatMasker), I want to run a PCA based on these regions between populations. How should I get the SNPs from either of these files (don't know which one is easier or better)?

[Istvan Albert]

what is an .align file? If you are using a specialized tool you need to look into the tool usage to figure out how to call SNPs

[mthm]

it is a an alignment of all the masked regions in the genome to the library consensus. the tool is RepeatMasker, I don't think it is designed to give SNPs, it is just for masking genomes to the repeat library.