[ensembl-dev] Variant Consequence Predictor

Stuart Meacham sm766 at cam.ac.uk
Fri Feb 25 11:05:49 GMT 2011

On 25/02/11 10:10, Will McLaren wrote:
> Basically, the results are OK for the alleles given - C/T gives a
> peptide change of A/T, whereas C/G gives a peptide change of A/P. So
> neither is necessarily "correct", it just depends what you want to
> interpret as being the observed alleles at that position. Of course,
> there is also the possible situation where in fact three alleles have
> genuinely been observed (C/G/T) at that position, which means they would
> both be correct!

Hi Will,

Thanks for your response. So now I have a problem because it seems what 
I have been doing is possibly invalid:

I have downloaded the tables I need from the DB 
homo_sapiens_variation_61_37f (variation_feature, transcript_variation, 
allele etc). I then link the variation_feature to the 
transcript_variation table to get the peptide change and to the allele 
table to get the relevant alleles for a given population. But what you 
are saying is that the peptide change in the transcript_variation table 
doesn't necessarily equate to the alleles in the allele table for any 
one given variation_feature?



> Hope this helps
> Will

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