[ensembl-dev] VEP populations frequency on output

[Will McLaren]

No, the cache that you download from our server contains the frequency data.

To recreate this with your own cache would be more difficult, as the
frequencies are imported from a separate data file.

Will


On 29 May 2013 11:20, <guillermo.marco at sistemasgenomicos.com> wrote:

> 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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> >
> >
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>
>
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