Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2021-06-01T06:05:10.320Z
Answers.LastActivityDate: 2021-06-01T06:05:10.320Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-26T23:12:21.133Z
Comments.Text: Its a fundamental question. It would be useful to understand a little more about your sample
Comments.UserDisplayName: M__
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-02-28T21:28:58.463Z
Comments.Text: It was long ago... What do you need to know?
Comments.UserDisplayName: juanjo75es
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-03-01T15:13:47.083Z
Comments.Text: thanks, let me think a lot and I will formulate a question on the site and drop a comment to flag notify you
Comments.UserDisplayName: M__
Tags: <vcf><variant-calling><covid-19><sars-cov-2>
Title: Consensus sequence from vcf file
ThreadText: # Consensus sequence from vcf file
  
  (Asked by: username_0 on 2021-05-31)
  
  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?
  
  **Tags:** vcf, variant-calling, covid-19, sars-cov-2
  
  > **Comments:**
  > **username_1**: Its a fundamental question. It would be useful to understand a little more about your sample  
  > **username_0**: It was long ago... What do you need to know?  
  > **username_1**: thanks, let me think a lot and I will formulate a question on the site and drop a comment to flag notify you  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2021-06-01. Score: 4
  
  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.
  
  
  ---
  
  