[ensembl-dev] VEP populations frequency on output

guillermo.marco at sistemasgenomicos.com guillermo.marco at sistemasgenomicos.com
Wed May 29 11:20:20 BST 2013


Ok sorry I didn't read part about cache.

So building a cache for homo sapiens ensembl 71 should do the trick. Both
--database and --cache options are compatible?

Thanks :)

> 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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>
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