[ensembl-dev] 1000 genomes

[Rebecca Ewing]

Hi

Is it possible to get minor allele frequencies from 1000 genomes using the Ensembl REST service?

Thanks

Rebecca

On 9 May 2014, at 10:38, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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