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How do we calculate nucleotide diversity when there are pairwise insertions/deletions ?
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I think the most standard approach is to just ignore them (only use biallelic SNPs). This seem good enough for most purposes.Originally posted by ymc View Post
I'm not a all sure how one would properly incorporate them. I suppose it depends on what exactly you are trying to really measure.
One simple approach would be to treat both SNPs and indels as generic markers/alleles. You wouldn't be calculating "nucleotide diversity" as such, more like "allelic diversity". One potential complexity is the different mutation rates, which could mess up estimating stuff like rates of divergence using the metric.
BTW: No one really cares about nucleotide diversity... It is easy to measure and correlated with or a proxy for stuff we do care about though.Comment
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