[ensembl-dev] [SPAM] - Re: Transcript variation alleles - - Bayesian Filter detected spam

Mon Feb 7 09:44:28 GMT 2011

Hi Gavin - The list of descriptions Andrea showed is our list of reasons for failing variations, we store failed variations and our reasons for failing them be looking in the failed_variation table. As of release 61, we no longer delete failed variations from the variation_feature table etc., but if you want to fetch them from the API you have to call $vdba->include_failed_variations(1) on a Variation DBAdaptor. You can then get the failed description from a failed Variation object using the get_all_failed_descriptions method.

Cheers,

Graham

On 7 Feb 2011, at 09:29, Oliver, Gavin wrote:

> Those were the statuses I was referring to Will.
>  
> Which leads me to ask – what were the statuses that Andrea listed?
>  
> Gavin
>  
> From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of Will McLaren
> Sent: 04 February 2011 15:04
> To: Andrea Edwards
> Cc: Dev at ensembl.org
> Subject: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - - Bayesian Filter detected spam
>  
> Hello,
>  
> I think there are some crossed wires here - validation_status is a property of a variation supplied to us by dbSNP.
>  
> Their descriptions are here:
>  
> http://www.ncbi.nlm.nih.gov/projects/SNP/snp_legend.cgi?legend=validation
> 
> The pictures are, in order:
>  
> cluster
> freq
> submitter
> doublehit
> hapmap
> 1000Genome
>  
> Will
> 
> On 4 February 2011 14:14, Andrea Edwards <edwardsa at cs.man.ac.uk> wrote:
> 
> 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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> 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.
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> 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.  
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