Question: Snpeff Not Annotating All Protein-Coding Transcripts??
gravatar for pablo.riesgo
7.1 years ago by
pablo.riesgo140 wrote:

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:"]



annotation • 2.1k views
ADD COMMENTlink modified 7.1 years ago • written 7.1 years ago by pablo.riesgo140
gravatar for pablo.riesgo
7.1 years ago by
pablo.riesgo140 wrote:

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.

ADD COMMENTlink written 7.1 years ago by pablo.riesgo140
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1778 users visited in the last hour