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

[Duarte Molha]

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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