Answers.Body: <p><em>Answer from @user438383, converted from comment:</em></p>
  <p>I would recommend checking out <a href="https://odelaneau.github.io/shapeit4/" rel="nofollow noreferrer">shapeit4</a> as it is able to integrate statistical phasing and read-based phasing like you are after. The manual page for WhatsHap might also be useful for you:</p>
  <p><a href="https://whatshap.readthedocs.io/en/latest/index.html" rel="nofollow noreferrer">https://whatshap.readthedocs.io/en/latest/index.html</a></p>
  
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Answers.CreationDate: 2021-07-14T11:14:23.450Z
Answers.LastActivityDate: 2021-07-14T11:14:23.450Z
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Body: <p>I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array.  I would like to merge the data together in the correct phase.  Since the exomes are already phased with read informed phasing, I don't want to rephase them because some of the phasing changes after doing this.  Is there a way to statistically phase genetic data that has already been partially phased?</p>
  <p>My data is in VCF format.</p>
  <p>Thanks</p>
  
Tags: <genomics><genotyping><exome><phasing>
Title: Phasing partially phased genomic data
ThreadText: # Phasing partially phased genomic data
  
  (Asked by: username_0 on 2020-03-29)
  
  I am trying to create an integrated callset with coding regions from phased exomes and noncoding regions from a genotyping array. I would like to merge the data together in the correct phase. Since the exomes are already phased with read informed phasing, I don't want to rephase them because some of the phasing changes after doing this. Is there a way to statistically phase genetic data that has already been partially phased?
  
  My data is in VCF format.
  
  Thanks
  
  **Tags:** genomics, genotyping, exome, phasing
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2021-07-14. Score: 1
  
  *Answer from @user438383, converted from comment:*
  
  I would recommend checking out [shapeit4](https://odelaneau.github.io/shapeit4/) as it is able to integrate statistical phasing and read-based phasing like you are after. The manual page for WhatsHap might also be useful for you:
  
  <https://whatshap.readthedocs.io/en/latest/index.html>
  
  
  ---
  
  