FST P-values for pairwise comparisons. Please Help.

[AJ-himb]

Hi there,

I have populations v2.59. 

I am calculating Fst statistics using the --fstats flag for a few populations and wanted to obtain pairwise fst comparisons for each population and their p-values.

The populations.fst_summary.tsv file provides the fst pairwise comparisons - however, Im not certain where i can find p-values for these comparisons? It is not listed in this file for me.

The populations.fst_Y-Z.tsv files for each pair of populations provide the FET p-values (well its coming out as Fisher's P in my files), however this is for each contig and not a p-value for a pairwise comparison (or am I missing something here?). For example: I'm comparing Fst for populations A,B,C and want a p-value for each set of populations A-B, B-C, and A-C along with the Fst values.

Here are the flags Im using in my script:

-H --vcf --structure --genepop --fstats --smooth --hwe --ordered-export

Thanks for your assistance!

[Catchen, Julian]

Hi, populations currently only provides Fst p-values for individual SNPs in pairwise comparisons of populations. It does not provide a statistical test for the whole genome (nor per contig).