[ensembl-dev] VEP populations frequency on output

[Will McLaren]

Hello,

--maf_1kg is only compatible with using the cache (--cache or --offline),
as this is where the frequencies are stored. I don't think it says as much
in the documentation; I will get this updated

To retrieve them from the database (using --database) would be extremely
slow; you should always use the cache if you can.

Regards

Will



On 28 May 2013 16:32, Guillermo Marco Puche <
guillermo.marco at sistemasgenomicos.com> wrote:

>  Hello !
>
> Currently I'm using *gmaf* and *maf_1kg* options.
>
> On my output AFR_MAF, AMR_MAF, ASN_MAF, EUR_MAF are always being reported
> empty "-". Just GMAF is being reported non empty.
> I want population frequency to be reported from 0 to maximum. I mean
> report all values I can.
>
> I've tried adding the following options:
>
> check_frequency    1
> freq_pop           any
> freq_freq          1
> freq_gt_lt         gt
> freq_filter        include
>
>
> This does include more lines to VEP output but all the columns still empty.
>
> Here's a variation example where other population should be reported:
>
>
> http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=1:11905298-11906308;v=rs144578530;vdb=variation;vf=35767060
>
> I don't know if this is a bug or I'm misunderstanding how it works. As I
> said I want all freqs to be reported without any minium or filter.
>
> Thanks !
>
> Best regards,
> Guillermo
>
>
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