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

[Oliver, Gavin]

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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