[ensembl-dev] Transcript variation alleles -

[Will McLaren]

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
>
>
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