[ensembl-dev] VEP populations frequency on output

[Will McLaren]

Correct, but if you just want to display the frequencies without filtering,
just use --gmaf and --maf_1kg - to do otherwise just wastes processing time!

Will


On 29 May 2013 09:14, Duarte Molha <Duarte.Molha at ogt.com> wrote:

> Correct me if I am wrong Will… but I believe that the arguments Guillermo
> is using are not adequate…****
>
> ** **
>
> Guillermo…If I understand correctly with your arguments you are requesting
> the script to check for frequencies and include all with a frequency above
> 1… Obviously there is no variant with a frequency above 1 J****
>
> ** **
>
> I think what you want is:****
>
> ** **
>
> check_frequency    1
> freq_pop           any
> freq_freq          1
> freq_gt_lt         lt   *(not gt”)*
> freq_filter        include****
>
> ** **
>
> Best regards****
>
> ** **
>
> Duarte****
>
> ** **
>
> ** **
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Guillermo Marco Puche
> *Sent:* 28 May 2013 16:33
> *To:* Ensembl developers list
> *Subject:* [ensembl-dev] VEP populations frequency on output****
>
> ** **
>
> 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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