text: user5190: 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?
  
  user77: Making a consensus sequence tends to involve some arbitrary decisions. In this case, the common practices are:
  
  Use the ancestral allele (this isn't always apparent)
  Use the most common allele
  Randomly choose
  
  I think 1 and 2 are generally preferred, with 2 being easier to implement.
  
original_text: 5190: <p>I am generating a consensus sequence for SARS-Cov-2. I am visually inspecting every candidate SNP in a pileup.</p>
  <p>Sometimes I find that there are two consistent variants for the same position, but I can only generate one consensus sequence.</p>
  <p>Which variant should I target:</p>
  <ul>
  <li>The majority variant</li>
  <li>The minoritarian one if I find that this SNP is under-reported in other public samples?</li>
  <li>Are both required</li>
  </ul>
  <p>What one is best practice?</p>
   77: <p>Making a consensus sequence tends to involve some arbitrary decisions. In this case, the common practices are:</p>
  <ol>
  <li>Use the ancestral allele (this isn't always apparent)</li>
  <li>Use the most common allele</li>
  <li>Randomly choose</li>
  </ol>
  <p>I think 1 and 2 are generally preferred, with 2 being easier to implement.</p>
  