[ensembl-dev] [SPAM] - Re: [SPAM] - Re: Transcript variation alleles - - Bayesian Filter detected spam - Email found in subject

Pablo Marin-Garcia pg4 at sanger.ac.uk
Mon Feb 7 14:33:58 GMT 2011

On Mon, 7 Feb 2011, Pontus Larsson wrote:

> Hi Gavin,
> Please note that in the current release (61), we are missing this validation 
> status for many variations. This happened because this data was not present 
> in the dbSNP data we had access to at the time of the import. (See the 'known 
> bugs' page http://www.ensembl.org/info/docs/knownbugs.html). I have put a 
> tab-separated file containing the current dbSNP validation statuses (exported 
> on Jan 20) for each rsId on the ftp site: 
> ftp://ftp.ebi.ac.uk/pub/software/ensembl/snp/human/e61_rsid_validation_status.txt.gz.

A) One question. could someone give some feedback on the following issue:

the validation_status file seems to have a inconsistency with the naming of the 
status. First seems that if it is only one status then has the prefix 'by' but 
not happening in 'hapmap' in rs11. The 'by' prefix get dropped when there are 
more than one status for a given SNP, but this does not happen in rs56. Could 
the 'by' be dropped so we can group by status better?

rs6     by freq
rs11    HapMap  # <====
rs12    by submitter
rs26    by cluster
rs27    1000Genome,2hits,cluster
rs56    by cluster,freq  # <====
rs57    HapMap,cluster

B) rs56 in ensembl_variation_60 has the status 'cluster,freq,1000Genome' but now 
'by cluster,freq'. Do you know why the 1000Genome status has been dropped in 
dbSNP? I have had the same issue with other SNPs where HapMap status disapeared 
when moving from latest ensembl in build 36 to ens_60 (b37), I assume that it 
was because a change in the dbSNP release. Are this missing status a bug in 
dbSNP or is there a good reason for the drop out?.


> You should be able to get the validation status from there. Apologies for 
> this inconvenience.
> Thanks
> /Pontus Larsson - Ensembl Variation
> On 07/02/2011 09:55, Oliver, Gavin wrote:
>> Thanks Graham/Fiona,
>> Really all I want to do at the moment is get a 'validated' or
>> 'unvalidated' value for each variation I consider.
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   Pablo Marin-Garcia
   Vertebrate Genomics
   Wellcome Trust Genome Campus

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