[ensembl-dev] Feature request (Allele variant Frequency)

[Duarte Molha]

Also, in addition to this, I could probably use the frequency flags to they
all information i need and then parse it later on...

like

check_frequency 1
freq_filter include
freq_freq 1
freq_gt_lt lt
freq_pop any

However, this is cumbersome and also removes all other variants from the
output that have no frequency information.

Thanks

Duarte

=========================
     Duarte Miguel Paulo Molha
         http://about.me/duarte
=========================


On Wed, May 22, 2013 at 11:57 AM, Duarte Molha <duartemolha at gmail.com>wrote:

> I am not sure if you have already addressed this question Will
> But I would like to request that a additional option be included for
> annotation output.
>
> Currently the GMAF of a given known variation is output with the --GMAF
> flag
>
> However, this does not give us the frequency of the seen allele on out
> sample.
>
> say their is a variation
>
> like so
> ref_allele       alt_alleles
> C                     A,T
>
> And our sample has a genotype 1,2
> and the GMAF gives us GMAF=A:0.2399
>
> In this case it is not possible to determine the allelic frequency of the
> other allele present in the sample.
>
> Ideally there should be a flag like --allele_freq that would five you the
> allele for the allele present in the sample.
> You must already be calculating this because you have fields for filtering
> variation based on their frequency in any given population ,
>
> Best regards
>
> Duarte
>
> =========================
>      Duarte Miguel Paulo Molha
>          http://about.me/duarte
> =========================
>
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