[ensembl-dev] 1000 genomes

[Laura Clarke]

If you would like remote non code base dependent access to the allele
frequencies from 1000 Genomes you can use tabix and an ftp url to get
specific genomic locations from our vcf files found here

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/

This is described in our faq

http://www.1000genomes.org/faq/how-do-i-get-sub-section-vcf-file

thanks

Laura

On 14 May 2014 10:58, Andy Yates <ayates at ebi.ac.uk> wrote:
> Hi,
>
> I'm sorry we do not support retrieving minor allele frequencies from the REST service. However this looks like it should be something we can add onto the service in the near future. I'll add it to our issue tracker and will try to keep you up to date as & when we make this information available.
>
> Andy
>
> ------------
> Andrew Yates - Ensembl Support Coordinator
> European Bioinformatics Institute (EMBL-EBI)
> European Molecular Biology Laboratory
> Wellcome Trust Genome Campus
> Hinxton
> Cambridge CB10 1SD
> Tel: +44-(0)1223-492538
> Fax: +44-(0)1223-494468
> http://www.ensembl.org/
>
> On 14 May 2014, at 09:41, Rebecca Ewing <rpe at sanger.ac.uk> wrote:
>
>> 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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