[ensembl-dev] variant effect prediction non_synonymous without alleles?

Graham Ritchie grsr at ebi.ac.uk
Fri Dec 24 10:53:46 GMT 2010


This bug has now been fixed, and the consequence_types and peptide_allele_strings have been fixed in the databases for the upcoming release 61. The fix is in CVS and will be included in the API release for 61, if anyone needs the fix sooner you can get a corrected version of Bio/EnsEMBL/Utils/TranscriptAlleles.pm (the only file altered) from the ensembl core repository (accessible on the web here: http://cvs.sanger.ac.uk/cgi-bin/viewvc.cgi/ensembl/modules/Bio/EnsEMBL/Utils/?root=ensembl).

Thanks for bringing this to our attention Stef.

Have a good Christmas!

Cheers,

Graham


On 23 Dec 2010, at 16:11, Graham Ritchie wrote:

> Hi Stef,
> 
> It looks like you have found a bug in our consequence calculation code! The peptide allele string in this case should be */Q and the consequence should be STOP_LOST (our as yet unreleased new consequence pipeline gets this right). We will endeavour to fix this as soon as we can. For the time being I think you should be able to treat all such results (where there is no reference peptide in the peptide allele string) as STOP_LOST events.
> 
> Sorry about this.
> 
> Cheers,
> 
> Graham
> 
> 
> On 23 Dec 2010, at 15:25, mailsvl at fastmail.fm wrote:
> 
>> Hi,
>> 
>> When I use the variant effect predictor (either online or with api) for
>> this snv:
>> 
>> 10_3181003_A/G 10:3181003 ENSG00000107959 ENST00000455371
>> NON_SYNONYMOUS_CODING 553 185 /Q rs2279217
>> 
>> You can see it predicts NON_SYN with only one allele in the change (
>> /Q), how is this possible?
>> 
>> Thanks,
>> Stef
>> 
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>> 
>> 
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