[ensembl-dev] VEP populations frequency on output

[Duarte Molha]

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 :)

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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