[ensembl-dev] How to distinguish variation types?

[Sarah Hunt]

Hi Gang,

Variation type values are held in the attrib table. You will need
something like this:

SELECT vf.variation_name, att.value FROM transcript_variation tv LEFT
JOIN variation_feature vf ON ( vf.variation_feature_id =
tv.variation_feature_id )  LEFT JOIN attrib att ON( att.attrib_id =
vf.class_attrib_id) WHERE tv.feature_stable_id =  'ENST00000419234' ;
+----------------+-------+
| variation_name | value |
+----------------+-------+
| rs74411430     | SNV   |
| rs34238389     | SNV   |
| rs146215394    | SNV   |
| rs11336940     | deletion     |
| rs139862452    | SNV          |
| rs111511913    | insertion    |


Best wishes,

Sarah

On Mon, Aug 13, 2012 at 9:12 AM, 陈岗 <danielchen06 at gmail.com> wrote:
> Hi All
>
> I am using SQL sentence to extract variation data with transcritp stable id,
> such as
>
> SELECT *
> FROM transcript_variation tv
> LEFT JOIN variation_feature vf ON ( vf.variation_feature_id =
> tv.variation_feature_id )
> WHERE tv.feature_stable_id =  'ENST00000419234'
>
> My question is how to distinguish variations types, such as invertion,
> deletion, indel, substitution and so on.
>
> Thanks
> --
> Gang Chen
> TILSI
> Taicang Institute For Life Science Information
> Address: A2/162, Renmin South Road, Taicang, 215400, Jiangsu Province,
> P.R.China
> Phone:（+86）512-82782588
>
>
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