Re: [Vcftools-help] What does the disclaimer under "Genotype Filters" on the Options page mean?

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

Hi Karen,

This is something I need to address systematically, so thanks for bringing
it up. Looking back through the code, I've made a list of the functions
where it looks like I've implemented genotype filtering.

Functions in which genotype filters have been implemented:
--plink
--012
--IMPUTE
--freq, --counts etc
--het
--hardy
--depth
--missing
--hap-r2 and related options
--singletons
--fst
--LROH
--relatedness
--recode

Functions in which genotype filters have not been implemented:
--ldhat, --ldhat-geno
--BEAGLE-GL
--geno-depth
--site-depth
--site-pi, --window-pi
--diff options

That's not to say that the genotype filter options have been particularly
well tested, so it would be very useful if you kept an eye out for anything
unusual. This is obviously an area where I'd like to improve things, so if
you do find any issues, please let me know and I'll try and ensure I fix it
asap. Also let me know if there are functions in the "not implemented" list
that you particularly need and I'll try and prioritise those.

Kind regards,

Adam


On 8 April 2011 01:52, Karen King <kar...@gs...> wrote:

> Under “Genotyping Filters” (options page):
>
>
>
> http://vcftools.sourceforge.net/options.html#geno_filter
>
>
>
> it says:
>
>
>
> The following options are currently inconsistently implemented, and should
> therefore be used with care.  Could someone please provide further insight?
>
>
>
> Does this mean there are known bugs?  Or, don’t combine them with other
> options?  Or, depending upon variations in file format, this may not work?
>
>
>
> I am trying to determine if use of this option would be appropriate for a
> project I am working on that requires genotype-level filtering.
>
>
>
> Thanks!
>
>
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-- 
Adam Auton
Post-Doctoral Research Scientist,
Wellcome Trust Centre for Human Genetics,
University of Oxford
Roosevelt Drive
Oxford
OX3 7BN
UK