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Old 03-01-2013, 06:41 AM   #1
Location: Spain

Join Date: Aug 2012
Posts: 22
Default SnpEff matching policy

Hi there,

I'm digging a little bit into SnpEff and everything works fine, but I have a doubt for which I didn't find an answer in any of the SnpEff papers/documentation.
I have a variant (rs4372192 ) in the intronic region of one gene (SAMD11) and it returns the annotations for all Ensembl non protein-coding transcripts in an interval of +/-5KB from this variant. Everything fine up to here.
But, not all the protein-coding transcripts for the gene (SAMD11) are matched, only one. Why is it not returning all protein-coding transcripts? Anybody knows if this is configurable? But, in any case is there any reason I should know for this working.

SnpEff output:
Ensembl visualization:


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Old 03-06-2013, 01:45 AM   #2
Location: Spain

Join Date: Aug 2012
Posts: 22

I will answer myself
A clue for this might be that the non-matched transcripts are marked as novel in Ensemble, instead of known. So, there are two alternatives: first, that the database SnpEff is using does not include these transcripts; or second that they are filtered out as they are less confident.
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