Answers.Body: <p>Here's my current understanding of the freemix metric output by verifyBamID. The freemix score is a measure of contamination that is calculated without knowing the genotypes of the individuals. In the paper it is equation (2), and the authors refer to it as the "sequence-only" method. However, in addition to the sequencing reads, it requires some knowledge of SNPs and their allele frequency from the population. They demonstrate in the paper that using the SNPs and allele frequency estimates from a different population actually reduces the estimated level of contamination.</p>
  
  <p>As for intuition for what equation (2) is measuring, imagine what would happen to the number of heterozygous sites detected if DNA from two different individuals was sequenced together. The total number of heterozygous sites would increase because it would count all sites where the two individuals are homozygous for opposite alleles or at least one of the two individuals is heterozygous. This would lead to an increased fraction of heterozygous sites over that expected from <a href="https://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle" rel="nofollow noreferrer">Hardy-Weinberg Equilibrium</a> (i.e. 2pq).</p>
  
  <p>Here's the <a href="https://groups.google.com/d/msg/verifybamid/oNMOfEZDwE4/AbVP_D-mbBEJ" rel="nofollow noreferrer">explanation of freemix</a> directly from the author, Hyun Min Kang:</p>
  
  <blockquote>
    <p>The key idea of FREEMIX estimate is to use excessive heterozygosity to estimate the level of contamination. Especially for common SNPs, you will observe higher fraction of heterozygous alleles than 2*p*(1-p), and it turns out that you can quantify the contamination very well if you know the population allele frequency already. If you do not have accurate population allele frequency information, than it would be harder to estimate FREEMIX parameters using verifyBamID.</p>
  </blockquote>
  
  <p>Additional sources:</p>
  
  <ul>
  <li><a href="http://genome.sph.umich.edu/wiki/Verifying_Sample_Identities_-_Implementation" rel="nofollow noreferrer">Verifying Sample Identities - Implementation</a></li>
  <li><a href="http://genome.sph.umich.edu/wiki/VerifyBamID#Interpreting_output_files" rel="nofollow noreferrer">Interpreting output files</a></li>
  <li><a href="https://groups.google.com/forum/#!forum/verifybamid" rel="nofollow noreferrer">verifyBamID Google Group</a></li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-08-25T21:30:44.297Z
Answers.LastActivityDate: 2017-08-25T21:30:44.297Z
Answers.UserDisplayName: John Blischak
Body: <p>We all have used freemix score at some stage to check contamination or swaps in our sequencing experiment, but can anyone once for all explain how the score is calculated? </p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-20T06:39:51.340Z
Comments.Text: Have you read [the paper](http://www.cell.com/ajhg/fulltext/S0002-9297(12)00478-8)? As an aside, we haven't all used VerifyBamID, it's mostly only useful in human experiments.
Comments.UserDisplayName: Devon Ryan
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-08-22T08:40:05.243Z
Comments.Text: @DevonRyan Yes I have read the paper but could not grasp how the freemix score is estimated? Posted the same question on Biostars about a year ago but did not get any answer!!
Comments.UserDisplayName: RJF
Tags: <sam><ngs>
Title: VerifyBamID freemix score
ThreadText: # VerifyBamID freemix score
  
  (Asked by: username_0 on 2017-08-19)
  
  We all have used freemix score at some stage to check contamination or swaps in our sequencing experiment, but can anyone once for all explain how the score is calculated?
  
  **Tags:** sam, ngs
  
  > **Comments:**
  > **username_1**: Have you read [the paper](http://www.cell.com/ajhg/fulltext/S0002-9297(12)00478-8)? As an aside, we haven't all used VerifyBamID, it's mostly only useful in human experiments.  
  > **username_0**: @username_1 Yes I have read the paper but could not grasp how the freemix score is estimated? Posted the same question on Biostars about a year ago but did not get any answer!!  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2017-08-25. Score: 4 | Accepted answer
  
  Here's my current understanding of the freemix metric output by verifyBamID. The freemix score is a measure of contamination that is calculated without knowing the genotypes of the individuals. In the paper it is equation (2), and the authors refer to it as the "sequence-only" method. However, in addition to the sequencing reads, it requires some knowledge of SNPs and their allele frequency from the population. They demonstrate in the paper that using the SNPs and allele frequency estimates from a different population actually reduces the estimated level of contamination.
  
  As for intuition for what equation (2) is measuring, imagine what would happen to the number of heterozygous sites detected if DNA from two different individuals was sequenced together. The total number of heterozygous sites would increase because it would count all sites where the two individuals are homozygous for opposite alleles or at least one of the two individuals is heterozygous. This would lead to an increased fraction of heterozygous sites over that expected from [Hardy-Weinberg Equilibrium](https://en.wikipedia.org/wiki/Hardy%E2%80%93Weinberg_principle) (i.e. 2pq).
  
  Here's the [explanation of freemix](https://groups.google.com/d/msg/verifybamid/oNMOfEZDwE4/AbVP_D-mbBEJ) directly from the author, Hyun Min Kang:
  
  > The key idea of FREEMIX estimate is to use excessive heterozygosity to estimate the level of contamination. Especially for common SNPs, you will observe higher fraction of heterozygous alleles than 2\*p\*(1-p), and it turns out that you can quantify the contamination very well if you know the population allele frequency already. If you do not have accurate population allele frequency information, than it would be harder to estimate FREEMIX parameters using verifyBamID.
  
  Additional sources:
  
  * [Verifying Sample Identities - Implementation](http://genome.sph.umich.edu/wiki/Verifying_Sample_Identities_-_Implementation)
  * [Interpreting output files](http://genome.sph.umich.edu/wiki/VerifyBamID#Interpreting_output_files)
  * [verifyBamID Google Group](https://groups.google.com/forum/#!forum/verifybamid)
  
  
  ---
  
  