I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup.
Sometimes I find that there are two consistent variants for the same position, but I can only generate one consensus sequence.
Which variant should I target:
- The majority variant
- The minoritarian one if I find that this SNP is under-reported in other public samples?
- Are both required
What one is best practice?