Hi all,
I have a little doubt about the SNPeff annotations:
Reading some documentation, I found the list of the Sequence Ontology Terms used to annotate the variants. There are 45 Terms, which are separated according their impact (LOW, MODERATE, HIGH and MODIFIER). I realized that many modifier terms are parents of higher impact terms, for example : the modifier term "coding_sequence_variant" is father of low impact term "synonymous_ variant"
My question is ¿Why it has to use parent terms ?, I mean, following the example above, if I have a variant that I know is changing a coding region, maybe I will know if that variation is synonymous or not. Why not only use the most down-level term?
I know there is a reason, but I would like to know.
Thanks in advance
I have a little doubt about the SNPeff annotations:
Reading some documentation, I found the list of the Sequence Ontology Terms used to annotate the variants. There are 45 Terms, which are separated according their impact (LOW, MODERATE, HIGH and MODIFIER). I realized that many modifier terms are parents of higher impact terms, for example : the modifier term "coding_sequence_variant" is father of low impact term "synonymous_ variant"
My question is ¿Why it has to use parent terms ?, I mean, following the example above, if I have a variant that I know is changing a coding region, maybe I will know if that variation is synonymous or not. Why not only use the most down-level term?
I know there is a reason, but I would like to know.
Thanks in advance