How to get SNPs (variant calling) from .gff or .align file?
I have masked several genomes each belonging to a separate population to a TE (transposon) library and I have got the gff file and the alignment files of the masked regions as outputs, 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)?
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