populations -f option

[brian simison]

I am using Stacks 2.2 and noticed a -f option in three of the examples, but do not see the -f option in the list of options for populations. What does -f do?

[Lars Viklund]

Based on a reading of the source code:

-f seems to be short for --fst_correction, which takes one of three corrections as an argument; p_value, bonferroni_win, bonferroni_gen.
If no -f is specified at all, a "none" correction is implicitly used.

"P-value correction."
"Bonferroni correction within sliding window.";
"Bonferroni correction across genome wide sites.";

As for what this actually means, I have no idea.

On 2018-09-29 17:53, brian simison wrote:

I am using Stacks 2.2 and noticed a -f option in three of the examples, but do not see the -f option in the list of options for populations. What does -f do?

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[brian simison]

Thank you.