Comparing diversity between two paralogs using a VCF file
I'm looking at two homeologs and trying to gain information about their potentially different evolutionary rates. There is a publicly available dataset in the form of a VCF file from whole genome sequencing of many different cultivars. Is there a way to get nucleotide diversity (and calculate for coding sequence, synonymous, nonsynonymous etc) or Ka/Ks values for the two paralogs?
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