[ensembl-dev] Question regarding MAF

Sarah Hunt seh at ebi.ac.uk
Tue Mar 6 17:16:20 GMT 2018


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

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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