[ensembl-dev] Question regarding MAF

[Anja Thormann]

Hi Duarte,

here is also some example code: 

my $va = $registry->get_adaptor('human', 'variation', 'variation');
$va->db->use_vcf(1);
my $variation = $va->fetch_by_name('rs770602');

my @alleles = @{$variation->get_all_Alleles};

foreach my $a (@alleles){
  my $freq = $a->frequency;
  if (defined $freq) {
    my $allele = $a->allele;
    my $population = (defined $a->population) ? $a->population->name : 'NA';
    print $population, ' ', $allele, ' ', $freq, "\n";
  }
}

More information on the Allele object is here http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Allele.html <http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1Allele.html>

HTH,
Anja

> On 6 Mar 2018, at 17:16, Sarah Hunt <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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