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

[Will McLaren]

Hello Gavin,

We apply some QC checking to the data that we import - we can assign
variations a status of "failed", along with a description of why this has
happened. You can access this through a variation object using the
failed_description() method. The list Andrea gave is the list of all
possible failed descriptions.

The API is configured such that by default data associated with failed
variations are not returned by methods that return more than one object
(e.g. fetch_all_by_Slice in VariationFeatureAdaptor); you can force the
retrieval of such data by retrieving the variation directly (e.g. using
fetch_by_name in VariationAdaptor), or by calling the method
include_failed_variations() on any adaptor from the Variation group
(functionality only available from e!61 onwards).

Thanks

Will


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 <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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>
> Limited, registered no. NI041550. Almac Discovery Limited, registered
>
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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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