[ensembl-dev] Fwd: 1000 genomes

[Will McLaren]

Hi Rebecca,

Have you considered using the Ensembl VEP?

It can annotate your VCF files with frequency data from 1000 genomes, as
well as a lot more:

http://www.ensembl.org/vep

With the added bonus of no coding required :-)

If you do still want to do this in Perl, you can retrieve the global (ie
combined across populations) frequency from a variation feature object in
our Perl API:

http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#genome

or frequencies from any sub-population via allele objects:

http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles

Hope that helps

Will McLaren
Ensembl Variation


On 9 May 2014 10:28, Rebecca Ewing <rpe at sanger.ac.uk> wrote:

> Hi Laura
>
> I want to search using data in vcf files from our pipeline and to add the
> information to the files, and I wondered if there was a better way than
> downloading all of the files.
>
> Thanks
>
> Rebecca
>
> On 9 May 2014, at 10:24, Laura Clarke <laura at ebi.ac.uk> wrote:
>
> > Hi Rebecca
> >
> > You can get the allele frequencies from Ensembl but you may find it
> > easier to get the numbers from the 1000 Genomes VCF files
> >
> >
> ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz
> >
> > thanks
> >
> > Laura
> >
> > On 9 May 2014 10:19, Rebecca Ewing <rpe at sanger.ac.uk> wrote:
> >>> Hi
> >>>
> >>> I am writing some perl code to compare some of our data against 1000
> genomes and get the minor allele frequencies. What would be the most
> efficient way to do this?
> >>>
> >>> Thanks
> >>>
> >>> Rebecca
> >>
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