[ensembl-dev] VEP populations frequency on output

[guillermo.marco at sistemasgenomicos.com]

Hello,

Tested today with cache as you said and all frequencies are now being
reported.

I would like to hide the Allele letter showing on GMAF column. Is that
possible? Even If i need to modify the VEP source code. Would really
appreciate :)

Thanks !

Regards,
Guillermo.

> 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****
>> >>>
>> >>> _______________________________________________
>> >>> Dev mailing list    Dev at ensembl.org
>> >>> Posting guidelines and subscribe/unsubscribe info:
>> >>> http://lists.ensembl.org/mailman/listinfo/dev
>> >>> Ensembl Blog: http://www.ensembl.info/
>> >>>
>> >>>
>> >> _______________________________________________
>> >> Dev mailing list    Dev at ensembl.org
>> >> Posting guidelines and subscribe/unsubscribe info:
>> >> http://lists.ensembl.org/mailman/listinfo/dev
>> >> Ensembl Blog: http://www.ensembl.info/
>> >>
>> >
>> >
>> > _______________________________________________
>> > Dev mailing list    Dev at ensembl.org
>> > Posting guidelines and subscribe/unsubscribe info:
>> > http://lists.ensembl.org/mailman/listinfo/dev
>> > Ensembl Blog: http://www.ensembl.info/
>> >
>>
>>
>>
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info:
>> http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog: http://www.ensembl.info/
>>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info:
> http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
>