Answers.Body: <p>The genotypes <span class="math-container">$\{0,1,2\}$</span> are mappings to the genotypes AA (homref), AB (heterozygous), BB (homalt) (from <a href="https://static-content.springer.com/esm/art%3A10.1038%2Fnbt.4042/MediaObjects/41587_2018_BFnbt4042_MOESM6_ESM.pdf" rel="nofollow noreferrer">supplementary</a> resources). This is also mapped to the number of alterations (e.g., 0 -&gt; 0 alterations -&gt; homref).</p>
  
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Body: <p>I am reading the Online methods of the <a href="https://www.nature.com/articles/nbt.4042" rel="nofollow noreferrer">demuxlet paper</a>.</p>
  <p>The genotype <span class="math-container">$g$</span> is taken from the set <span class="math-container">$\{0, 1, 2\}$</span>, defined as &quot;the true genotype of the sample corresponding to <span class="math-container">$c$</span>-th droplet at <span class="math-container">$v$</span>-th variant&quot;.
  What is the mapping between these values and the corresponding genotype?</p>
  <p>Each variant is modeled using a binomial with <span class="math-container">$n=2,p=\frac{g}{2}$</span>, so I would assume that 1 is heterozygous, 0 is homozygous REF and 2 homozygous ALT. Is this assumption correct?</p>
  
Tags: <single-cell><genotyping><demultiplexing>
Title: Definition of genotype in demuxlet
ThreadText: # Definition of genotype in demuxlet
  
  (Asked by: username_0 on 2022-11-21)
  
  I am reading the Online methods of the [demuxlet paper](https://www.nature.com/articles/nbt.4042).
  
  The genotype $g$ is taken from the set $\{0, 1, 2\}$, defined as "the true genotype of the sample corresponding to $c$-th droplet at $v$-th variant".
  What is the mapping between these values and the corresponding genotype?
  
  Each variant is modeled using a binomial with $n=2,p=\frac{g}{2}$, so I would assume that 1 is heterozygous, 0 is homozygous REF and 2 homozygous ALT. Is this assumption correct?
  
  **Tags:** single-cell, genotyping, demultiplexing
  
  
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  ## 1 answers
  
  ### Answer by username_0 on 2022-11-30. Score: 1 | Accepted answer
  
  The genotypes $\{0,1,2\}$ are mappings to the genotypes AA (homref), AB (heterozygous), BB (homalt) (from [supplementary](https://static-content.springer.com/esm/art%3A10.1038%2Fnbt.4042/MediaObjects/41587_2018_BFnbt4042_MOESM6_ESM.pdf) resources). This is also mapped to the number of alterations (e.g., 0 -> 0 alterations -> homref).
  
  
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