[ensembl-dev] 1000 Genomes SNPS

[cj5 at sanger.ac.uk]

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
>>
>>
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>