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

[Will McLaren]

Hi Duarte,

This would only really work with the GMAF, since that is the only one for
which the allele is provided.

The other frequencies (at least those stored in the cache) are specifically
the minor allele frequency - the particular allele to which this refers is
not stored, so your idea would not work, or at least not reliably.

If retrieving frequencies from the database, you can get the allele, but
this is very slow for large datasets so I don't think it would be worth
implementing.

You could always jump in with a plugin - all of the frequency stuff you'll
find cached on the variation_feature object in various hash structures -
just dump one out in the debugger and you'll see the structure.

Will


On 23 May 2013 09:26, Duarte Molha <Duarte.Molha at ogt.com> wrote:

> Any views on this?****
>
> ** **
>
> Thanks****
>
>
> Duarte****
>
> ** **
>
> ** **
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Duarte Molha
> *Sent:* 22 May 2013 13:17
> *To:* Ensembl
> *Subject:* Re: [ensembl-dev] Feature request (Allele variant Frequency)***
> *
>
> ** **
>
> 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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