populations nucleotide diversity

[ctda...@gmail.com]

Hi 

I am trying to obtain nucleotide diversity for a number of island populations. When I run the '-k' option with a population map I get a bunch of outputs for population pairs - I'm not sure how that helps me as I want nucleotide diversity within populations. How do I get nucleotide diversity for my individual populations?

Also, what do the output headers mean and where is the documentation for that? e.g. column headers such as "Phi_st" and "Smoothed" and "phi_st".

Finally, nucleotide diversity is denoted by π (pi) - yet the outputs say "phi", are these the same thing?

Many thanks

Clive

[ctda...@gmail.com]

Can I just add that I realise that I just realised that the '-k' option overwrote my *.fst_TAXA.tsv files and that pi is given in those files. But these are still paired population files and I want nuc div for individual populations

Thanks

C

[Julian Catchen]

Hi,

You will want to spend some time looking at the file formats as
explained in the manual:

http://catchenlab.life.illinois.edu/stacks/manual/#pfiles

You are looking for pi in the wrong place (look in the sumstats or
sumstats_summary files, which contain summary statistics for each
individual population). F statistics are a separate category from the
summary statistics (and are computed pairwise between populations).
Finally, there is also a distinction in SNP-based summary statistics and
haplotype-based ones. Haplotype statistics use the whole RAD locus as a
marker instead of individual SNPs and Phi_st or Φst are in the haplotype
category.

julian

ctda...@gmail.com wrote:
> Hi
>
> I am trying to obtain nucleotide diversity for a number of island
> populations. When I run the '-k' option with a population map I get a
> bunch of outputs for population pairs - I'm not sure how that helps me
> as I want nucleotide diversity within populations. How do I get
> nucleotide diversity for my individual populations?
>
> Also, what do the output headers mean and where is the documentation for
> that? e.g. column headers such as "Phi_st" and "Smoothed" and "phi_st".
>

> Finally, nucleotide diversity is denoted by /π /(pi) - yet the outputs

[ctda...@gmail.com]

Ah thank you

Clive