[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?
Cheers
Stuart
>
> Hope this helps
>
> Will
>
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