[ensembl-dev] [SPAM] - Re: [SPAM] - Re: Transcript variation alleles - - Bayesian Filter detected spam - Email found in subject
Oliver, Gavin
gavin.oliver at almacgroup.com
Mon Feb 7 09:55:19 GMT 2011
Thanks Graham/Fiona,
Really all I want to do at the moment is get a 'validated' or
'unvalidated' value for each variation I consider.
-----Original Message-----
From: Graham Ritchie [mailto:grsr at ebi.ac.uk]
Sent: 07 February 2011 09:44
To: Oliver, Gavin
Cc: Will McLaren; Andrea Edwards; Dev at ensembl.org
Subject: [SPAM] - Re: [ensembl-dev] [SPAM] - Re: Transcript variation
alleles - - Bayesian Filter detected spam - Email found in subject
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=validatio
n
>
> 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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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.
>
> 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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