[ensembl-dev] Transcript variation alleles -

[Andrea Edwards]

Gavin

I believe the validatation statuses are just pass and fail

If you query the variation schema directly you can find the reasons for 
failure when a variation is imported from say dbSNP

mysql> select description from failed_description;
+--------------------------------------------------------+
| description                                            |
+--------------------------------------------------------+
| Variation maps to more than 3 different locations      |
| None of the variant alleles match the reference allele |
| Variation has more than 3 different alleles            |
| Loci with no observed variant alleles in dbSNP         |
| Variation does not map to the genome                   |
| Variation has no associated sequence                   |
+--------------------------------------------------------+
6 rows in set (0.06 sec)

As will has said, they map all variants to the positive strand and make 
sure at least one of the variant alleles exists at the base position in 
the forward strand. If this failed you would get the error 'None of the 
variant alleles match the reference allele.' I think the others are 
fairly self explanatory though i'm not sure how a variant could have no 
associated sequence if it was imported from dbSNP






On 02/02/2011 15:20, Oliver, Gavin wrote:
> Thanks Graham -
>
> Can you also tell me where to find information on the meaning of the
> possible validation statuses?
>
>
>
> -----Original Message-----
> From: Graham Ritchie [mailto:grsr at ebi.ac.uk]
> Sent: 02 February 2011 15:12
> To: Oliver, Gavin
> Cc:dev at ensembl.org
> Subject: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email
> found in subject
>
> Hi Gavin,
>
> The alleles of a transcript variation always represent the genomic base
> change.
>
> Cheers,
>
> Graham
>
> Ensembl variation
>
>
> On 2 Feb 2011, at 15:02, Oliver, Gavin wrote:
>
>> Hi,
>>
>> When I pull transcript variation alleles via the API, does the allele
> shown (e.g. A/T) represent the genomic base change, or the
> transcriptomic one?
>>
>> Gavin
>>
>>
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