[ensembl-dev] Question regarding MAF

[Duarte Molha]

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



[image: --]
Duarte Molha
[image: https://]about.me/duarte
<https://about.me/duarte?promo=email_sig>

On 6 March 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
>
> 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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