[ensembl-dev] VEP populations frequency on output

[guillermo.marco at sistemasgenomicos.com]

Hello,

Before testing freq filtering I was using --gmaf and --maf_1kg as only
frequency population options.

But because I've never seen an output file reporting any AFR_MAF, AMR_MAF,
ASN_MAF, EUR_MAF with any value other than "-" (empty) that's why I was
asking.

Does VEP do any kind of default filtering or threshold value for those
output columns?

Thanks.

Regards,
Guillermo.



> 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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