Re: [Vcftools-help] Fst and non-called samples

[Adam A. <ada...@gm...>]

Could you give an example? What version of vcftools are you using? In my
tests, vcftools includes sites with some missing data, so I'm not sure I'm
understanding the issue.

Thanks.

Adam

On Wed, Apr 29, 2015 at 6:02 PM, Travis Collier <tra...@gm...>
wrote:

> Ugh...
> weir-fst is pretty broken when working from a vcf with non-called (./.)
> genotypes.
> If any sample (not just the ones being included in the weir-fst-pops) is
> uncalled, then it skips position.  That is very broken IMO.
>
> One can somewhat work around it by using --keep to filter for just the
> samples included in the weir-fst-pops, but that leads to the still
> 'not-very-nice' behaviour of skipping positions where any sample in those
> pops is uncalled.
>
> It really should be treating uncalled genotypes / missing data properly.
> I thought one of the big points of Weir and Cockerham's Fst estimator was
> handling situations where the sample sizes are unequal and/or variable.
>
> I don't have the time to work out a proper fix at the moment, but really
> wanted folks to be aware of the problem.
>
>
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-- 
Adam Auton
Assistant Professor,
Department of Genetics,
Albert Einstein College of Medicine,
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