changing the variant fraction parameters in UG or HC - for RNA editing identification
we are trying to use th ecariant callers (UG or HC) for identifying RNA editing sites in RNA-Seq samples.
As the fraction of the variants (i.e. editing levels) can range from 0% to 100% (as oppose to 0%,50% or 100% when dealing with genomic variants), we are wondering if there is any argument in the UG/HC walkers that can be tuned according to our choice, that determines the variant fraction?
in their paper, Ramaswami et al 2013 (Nature Methods, Vol 10(2) p.128) used "stand_call_conf 0" and "stand_emit_conf 0", and then performed filtering according to their ampirical choices.
does these arguments determine the fraction of variant reads? (we could not understand exactly what these arguments mean)
Will appreciate your help