I have gone through some of the publications and done a literature survey, I have a basic doubt and seek guidance from the Computational Genetic persons or Mol. Biology persons.
What is Ref and Alt ? Does all variations are considered as mutations ? It may be likely pathogenic or pathogenic or neutral but it is wise to call them mutations ? After doing annotation using Annovar, some REF and ALT are non-variations (G > G) but they are reported as mutation in PolyPhen, SIFT and other databases.
Could anyone help me to understand this concept ?