[ensembl-dev] precedence of snp consequences

[Andrea Edwards]

Hi

You replied at the same time as me :)

I was simply trying to look for the 'worst consequence' in the 
snp_effect_predictor script to try and mimic the results you could get 
from the api with this script. I wasn't trying to find it for any 
biological reason - just to get parity between the 2. Though of course 
if the perl api has employed some logic on the list of possible 
consequences for the transcript in the context of that transcript, i 
didn't want to lose that possible enrichment of my data by switching to 
the snp_effect_predictor. Naturally you look at the consequences in more 
detail manually but, with the number of SNPs in a data set, i considered 
any hints in the right direction from a value-added integrator such as 
ensembl with lots of knowledge at its fingertips to be worth keeping 
hold of.

Cheers





On 24/01/2011 09:55, Fiona Cunningham wrote:
>   Hello Andrea,
>
> You should really be considering the consequence of the particular
> variant  for each transcript that it falls in. This is the correct
> thing to do from a biological point of view and this is what the
> variant effect predictor does.
> For display purposes on the region in detail page only, as we display
> of SNPs track that is independent of the transcripts but you should
> take the transcript in to consideration when calculating your
> consequences. we have internally produced a ranking of consequence so
> that the "worst" consequence is used to colour code of variants on
> this page but this really is only for display purposes only as an
> indication, and has not been independently scientifically verified.
> There is no such thing as an "main consequence".
>
> Best regards,
>
> Fiona
>
> ------------------------------------------------------
> Fiona Cunningham
> Ensembl Variation Project Leader, EBI
> www.ensembl.org
> www.lrg-sequence.org
> t: 01223 494612 || e: fiona at ebi.ac.uk
>
>
>
> On 23 January 2011 20:01, Andrea Edwards<edwardsa at cs.man.ac.uk>  wrote:
>> Hello
>>
>> What are the rules that ensembl uses to determine the display_consequence of
>> a SNP from all of its possible consequences?
>>
>> As an example I am looking at a SNP whose main consequence
>> (display_consequence) = 3PRIME_UTR and all consequences (consequence_type)
>> are given as NMD_TRANSCRIPT, 3PRIME_UTR
>>
>> Is there a list or ranking you use for consequences to say that 3PRIME_UTR
>> is more important than NMD_TRANSCRIPT?
>>
>> Will the main consequence always be last in the list of the consequence_type
>> property?
>>
>> One reason I ask is because I am trying to apply the same consequence
>> ranking to the results returned by the snp_effect_predictor script. That
>> script returns one row/line for every consequence in the consequence_type
>> field and the order of the consequences in the rows returns seems to be the
>> same as the order of the consequences in the consequence_type property. If
>> the display_consequence is always last in the list then i can assume the
>> last row returned for a transcript variant is the 'main consequence'
>>
>> thanks
>>
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