Re: [Vcftools-help] How is the WEIGHTED_FST column calculated?

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Weighted FST is calculated using the Weir and Cockerham 1984 estimator.

Kind regards,

Adam

On Fri, Feb 20, 2015 at 10:23 AM, Giovanni Marco Dall'Olio <
dal...@gm...> wrote:

> Hello,
> If I run vcftools with --weir-fst-pop and the two options for calculating
> it by windows (--fst-window-size , --fst-window-step), I get a table like
> the following:
>
> CHROM   BIN_START       BIN_END N_VARIANTS      WEIGHTED_FST    MEAN_FST
> 2       130000001       130001000       8       0.165585        0.0753848
> 2       130001001       130002000       10      0.145083        0.0327587
>
> How is the Weighted Fst column calculated? I see that it appears only when
> using the windowing option. It must be based on the mean Fst of the window
> weighted by another factor, but I could not understand which is this this
> other factor. Dividing or multiplying the mean Fst by the number of
> variants doesn't return the same result.
>
> Sorry if this is a silly question, but I couldn't find it in the
> documentation or in this mailing list.
> Thanks in advance!
> Gio
>
>
>
> --
> Giovanni Marco Dall'Olio, PhD
> Division of Cancer Studies,
> King's College of London (UK)
>
> My blog on bioinformatics: http://bioinfoblog.it
>
>
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-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
1301 Morris Park Avenue,
Price Center, Room 353B,
Bronx, New York 10461

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