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

[Duarte Molha]

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<mailto: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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