<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>

CC BY-SA 4.0
2021-06-01T06:05:10.320Z
2021-06-01T06:05:10.320Z
Devon Ryan
<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>

CC BY-SA 4.0
2022-02-26T23:12:21.133Z
Its a fundamental question. It would be useful to understand a little more about your sample
M__
CC BY-SA 4.0
2022-02-28T21:28:58.463Z
It was long ago... What do you need to know?
juanjo75es
CC BY-SA 4.0
2022-03-01T15:13:47.083Z
thanks, let me think a lot and I will formulate a question on the site and drop a comment to flag notify you
M__
<vcf><variant-calling><covid-19><sars-cov-2>
Consensus sequence from vcf file
# 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  

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## 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.


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