Answers.Body: <p>Yes. <a href="https://www.mdpi.com/2075-1729/12/12/2030#B16-life-12-02030" rel="noreferrer">Phasing data leads to a better imputation accuracy</a>. More specifically:</p>
  <ul>
  <li>Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and the target dataset.</li>
  <li>Using phased data, the computational time of imputation is significantly reduced.</li>
  <li>Having haplotypes (phased data) helps imputing variants that were not genotyped (missing variants/genotypes).</li>
  </ul>
  <p><a href="https://www.nature.com/articles/ncomms9111" rel="noreferrer">This paper</a> based on the UK10K data has some actual numbers describing imputation accuracy of phased vs unphased data.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-10-11T09:23:58.907Z
Answers.LastActivityDate: 2023-10-11T09:23:58.907Z
Answers.UserDisplayName: JRodrigoF
Body: <p>If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-10T08:36:55.407Z
Comments.Text: What method do you want to use - this likely makes a difference.
Comments.UserDisplayName: user438383
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-10T17:56:22.103Z
Comments.Text: @user438383 Beagle/Eagle
Comments.UserDisplayName: BigMistake
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-10T17:56:42.520Z
Comments.Text: @user438383 but I'd also be interested in other methods if someone happens to know those too
Comments.UserDisplayName: BigMistake
Tags: <microarray><wgs><imputation><phasing>
Title: Does phasing improve imputation quality?
ThreadText: # Does phasing improve imputation quality?
  
  (Asked by: username_0 on 2023-10-10)
  
  If so, by about how much? I want to know the downsides of skipping the phasing step on human microarray and WGS data.
  
  **Tags:** microarray, wgs, imputation, phasing
  
  > **Comments:**
  > **username_1**: What method do you want to use - this likely makes a difference.  
  > **username_0**: @username_1 Beagle/Eagle  
  > **username_0**: @username_1 but I'd also be interested in other methods if someone happens to know those too  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-10-11. Score: 6 | Accepted answer
  
  Yes. [Phasing data leads to a better imputation accuracy](https://www.mdpi.com/2075-1729/12/12/2030#B16-life-12-02030). More specifically:
  
  * Improves allele matching: Correct phased data ensures that alleles are matched correctly between the reference panel and the target dataset.
  * Using phased data, the computational time of imputation is significantly reduced.
  * Having haplotypes (phased data) helps imputing variants that were not genotyped (missing variants/genotypes).
  
  [This paper](https://www.nature.com/articles/ncomms9111) based on the UK10K data has some actual numbers describing imputation accuracy of phased vs unphased data.
  
  
  ---
  
  