Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()

Question

[S]

I'm getting different Fst values when I use vcftools --weir-fst-pop vs. the varcomp.glob() function from the R hierfstats package. I'm not sure why because they both calculate Fst based on Weir & Cockerham's 1984 paper. Can someone please explain why?

Vcftools documentation states that this is calculated on a "per-site basis." (link: https://vcftools.github.io/man_latest.html)

Hierfstats' varcomp.glob() documentation states that this function "will produce the estimation of the variance components for each locus and overall, as well as the matrix of hierarchical F - statistics". (link: https://rdrr.io/cran/hierfstat/man/varcomp.glob.html)

Fst, group 1: vcftools = 0.079; hierfstats = 0.

Fst, group 2: vcftools = 0.049; hierfstats = 0.005.

Thanks so much

Answer 1

[S]

Just found this post comparing methods for computing Fst. These differences could be related to differences in how each tool handles missing data, among other things: https://thierrygosselin.github.io/assigner/articles/web_only/fst_comparisons.html