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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. What is the best practice? Getting always the majoritarian variant or getting the minoritarian one if I find that this SNP is under-reported in other public samples? apart of which one is best practice, are both practices legit?

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Making a consensus sequence tends to involve some arbitrary decisions. In this case, the common practices are:

  1. Use the ancestral allele (this isn't always apparent)
  2. Use the most common allele
  3. Randomly choose

I think 1 and 2 are generally preferred, with 2 being easier to implement.

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