[ensembl-dev] VEP Frequency annotation

[Will McLaren]

Hi Duarte,

You could achieve a similar thing by putting your frequencies in a
BED-like or BigWig file, and load it with the VEP using --custom. See
the documentation for details
http://www.ensembl.org/info/docs/variation/vep/vep_script.html#custom.

You could use VCFtools to calculate the frequencies, or parse them out
of a VCF (if they're already there in the INFO field) using a simple
perl script. I have done so with the 1000 Genomes VCF files and it
works great.

You could then access this frequency data through a plugin.

The problem with adding the frequencies used to filter is that often
there are multiple frequencies pulled from the database; we don't have
one "global" frequency to use (although in future this may be possible
using a global frequency from the 1000 Genomes for example), and the
output may get messy.

Hope this helps

Will

On 4 May 2012 11:00, Duarte Molha <Duarte.Molha at ogt.co.uk> wrote:
> Dear Devs.
>
>
>
> I have another question/feature request regarding the VEP script.
>
>
>
> I know that we can use the script to filter the variations according to
> allelic frequency. It would be very useful if one option could be added so
> that it outputs the frequency for the allele (whatever it maybe) without
> doing any filtering. Currently I have made a workaround by preprocessing all
> allelic frequencies for v64 and then changed the VEP script to add that
> information to the RSID field. Not that you allow plugins I believe I can
> make a plugin to do this without having to hack the VEP code. However it
> would be very usefull, since you already have code in place to check for
> frequencies if you could output the frequencies without forcing any
> filtering.
>
>
>
> Best regards
>
>
>
> Duarte Molha
>
>
>
>
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