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

Fiona Cunningham fiona at ebi.ac.uk
Mon Feb 7 09:42:39 GMT 2011


 Hi Gavin,

The validation status is something supplied by dbSNP normally
associated with the manner in which the variant was discovered (HapMap
Project, 1000 genomes, frequency, etc). What Andrea is referring to
are the warnings that Ensembl adds during our pipeline process when we
discover that a variant record looks dubious, i.e. it falls in one of
the following categories:
> 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                   |
> +--------------------------------------------------------+

Up until release 61 we used to delete the data associated with these
variants but now we leave it in the database. In general the behaviour
should be as it was before release 61 unless you explicitly ask for
the failed variants as well. For example you can see these "failed
variants" by turning on the track in region in detail or by explicitly
asking for them in the API, see this page for more information:
http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#failed_variations


Best regards

Fiona

------------------------------------------------------
Fiona Cunningham
Ensembl Variation Project Leader, EBI
www.ensembl.org
www.lrg-sequence.org
t: 01223 494612 || e: fiona at ebi.ac.uk



On 7 February 2011 09:29, Oliver, Gavin <gavin.oliver at almacgroup.com> 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
>
>
>
>
>
> The contents of this message and any attachments to it are
>
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> advise the sender.
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>
>
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>
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>
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>
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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.
>
>
>
> 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
>
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