[ensembl-dev] Fwd: Re: 1000 Genomes SNPS

[Andrea Edwards]

I used v61

C:\Documents and Settings\Administrator>mysql -h ensembldb.en
ous -P 5306
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 41648834
Server version: 5.1.34-log Source distribution

Type 'help;' or '\h' for help. Type '\c' to clear the buffer.

mysql>  use homo_sapiens_variation_61_37f;
Database changed
mysql>  select distinct name from variation_set;
+--------------------------------------------+

On 02/03/2011 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
>>>
>>>
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>>>
>
>
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