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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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