I am trying to calculate genetic distances between individuals of a large genotyping-by-sequencing dataset. So far, I have read in the data, by reading in the vcf file and converting it to a `genlight` object with functionality from `adegenet`. So far, I have tried running the standard `dist` function from base R and `bitwise.dist` from the `poppr` package. With the standard settings those yield different results. Only when I put `scale_missing=TRUE`, I get the the same results as in `dist`. This behavior is mentioned in the documentation of `bitwise.dist`, so I expect as much.

To illustrate what is happening:

library(poppr)

library(adegenet)

dat