[ensembl-dev] 1000 Genomes SNPS

[Stuart Meacham]

Hello,

If you are interested in the Phase 1 release data for CEU population of 
the 1000 Genomes project (not yet in Ensembl as far as I know) then I 
have developed a web app to the processed data to augment that already 
in Ensembl:

http://robosnp.org

RoboSNP displays data on a transcript by transcript basis so may not be 
exactly what you are looking for but feel free to have a play bearing in 
mind that it is a beta release and likely buggy so I take no 
responsibility for errors! Bug reports however would be appreciated.

Enabling cookies is a necessity . . .

Cheers

Stuart

On 02/03/11 16:17, cj5 at sanger.ac.uk wrote:
> Hi
>
> Many thanks Andrea and Pontus for your help with this. May I ask which
> version of the API you are both using to get your variation sets?
>
> I am using version 60, and I got a list of available sets by iterating
> get_all_sub_VariationSets within fetch_all_top_VariationSets, I found the
> following 1000 genomes sets only:
> 1000 genomes
>          1000 genomes - Low coverage
>          1000 genomes - Trios - YRI
>          1000 genomes - Trios - CEU
>
> Thanks
> Chris
>
>> Hi Chris,
>>
>> Andrea is right, we have grouped these variations together into various
>> variation sets. For example, you can get all variations belonging to the
>> different pilots from the sets '1000 genomes - Low coverage', '1000
>> genomes
>> - High coverage - Trios' and '1000 genomes - High coverage exons' for
>> pilot
>> 1,2 and 3, respectively. You'll need to use the VariationSet and
>> VariationSetAdaptor modules for this. It is not possible to retrieve the
>> variations conditional on submission date.
>>
>> As Andrea points out, if you call the 'get_all_Variations' method on a
>> VariationSet object, the API will create all variation objects and return
>> them. For large sets like these, this can easily cause you to run out of
>> memory but you can use the 'get_Variation_Iterator' method to get an
>> Iterator object and iterate over the variations instead.
>>
>> /Pontus
>>
>>
>>
>> 2011/3/2<cj5 at sanger.ac.uk>
>>
>>> Hi,
>>> Is it possible using the variations API to get a list of SNPS which have
>>> been submitted from the 1000 Genomes project?
>>>
>>> I have a vague idea that it should be possible to retrieve such a list
>>> using the SS (submission) ID and/or the validation status, however I am
>>> unsure of the details and what version of the API should be used.
>>>
>>> The latest 100 genomes pilot release (2010_07) would be great, but any
>>> earlier release would also be useful.
>>>
>>> Thanks
>>> Chris
>>>
>>>
>>> _______________________________________________
>>> Dev mailing list
>>> Dev at ensembl.org
>>> http://lists.ensembl.org/mailman/listinfo/dev
>>>
>
>
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