[ensembl-dev] VEP populations frequency on output
Guillermo Marco Puche
guillermo.marco at sistemasgenomicos.com
Tue May 28 16:32:50 BST 2013
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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