[ensembl-dev] Question regarding MAF

[Anja Thormann]

The files are described in a config file: https://github.com/Ensembl/ensembl-variation/blob/release/91/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json <https://github.com/Ensembl/ensembl-variation/blob/release/91/modules/Bio/EnsEMBL/Variation/DBSQL/vcf_config.json>

You don’t need to have the files locally. The files are all availably remotely. If you want to keep your files locally you need to download the files and update the vcf_config,json with the new location.

HTH,
Anja

> On 6 Mar 2018, at 17:56, Duarte Molha <duartemolha at gmail.com> wrote:
> 
> I think that just introduced a can of worms into my script. Where are these VCF files stored? I am running the code from a locally stored ensembl database.
> 
> Do I need to retrieve additional data when creating my database to get these files?
> 
> Thanks
> 
> Duarte
> 
>  
> 
> Duarte Molha
> about.me/duarte
> 
>  <https://about.me/duarte?promo=email_sig> 				
> 
> 
> On 6 March 2018 at 17:16, Sarah Hunt <seh at ebi.ac.uk <mailto:seh at ebi.ac.uk>> wrote:
> 
> Hi Duarte,
> 
> We store large scale genotype and frequency data in VCF now, so you need to set an extra flag on the API:
> $variation_adaptor->db->use_vcf(1);
> 
> to access it. More details are available here:
> 
> http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag <http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#ag>
> 
> Best wishes,
> 
> Sarah
> 
> 
> On 06/03/2018 17:00, Duarte Molha wrote:
>> Hi Guys
>> 
>> I am retrieving variations using the API that have a certain value of MAF
>> 
>> for example rs770602
>> 
>> If you retrieve this variation 
>> 
>> like so: $vf->minor_allele_frequency
>> 
>> it reports a MAF of 0.495807
>> 
>> but when I get each allele 
>> 
>> my @alleles = @{$vf->get_all_Alleles};
>> 
>> and I cycle through them, their frequency is undef
>> 
>> foreach my $a (@alleles){
>> 	my $freq = $a->frequency();
>> 	print  $freq;
>> }
>> 
>> How do I retrieve the frequency calculated for each individual alleles on the variation?
>> 
>> Many thanks
>> 
>> Duarte
>> 
>> 
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> 
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