[ensembl-dev] Transcript variation alleles -

Andrea Edwards edwardsa at cs.man.ac.uk
Fri Feb 4 14:14:31 GMT 2011


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
>> The contents of this message and any attachments to it are
> confidential and may be legally privileged. If you have received this
> message in error, you should delete it from your system immediately and
> advise the sender.
>> Almac Group (UK) Limited, registered no. NI061368.  Almac Sciences
> Limited, registered no. NI041550. Almac Discovery Limited, registered
> no. NI046249.  Almac Pharma Services Limited, registered no. NI045055.
> Almac Clinical Services Limited, registered no. NI041905.  Almac
> Clinical Technologies Limited, registered no. NI061202.  Almac
> Diagnostics Limited, registered no. NI043067.  All preceding companies
> are registered in Northern Ireland with a registered office address of
> Almac House, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.
>> Almac Sciences (Scotland) Limited, registered in Scotland no.
> SC154034.
>> Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac
> Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are
> Delaware limited liability companies and Almac Group Incorporated is a
> Delaware Corporation.  More information on the Almac Group can be found
> on the Almac website:www.almacgroup.com
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
> mailman/listinfo/dev
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20110204/f28d3639/attachment.html>

More information about the Dev mailing list