I’m trying to decide on thresholds for calling consensus sequence for SARS-COV-2 samples.
For variants with frequencies above 0.7 - of course I will include them in the consensus.
But what do you recommend regarding borderline variants? For example a base having 60% reference base and 40% alternative?
should I call a wobble for this position using the IUPAC nucleotides? or should I call N? or maybe the reference nucleotide?
Thank you very much!