Answers.Body: <p><a href="https://odelaneau.github.io/shapeit4/" rel="nofollow noreferrer">shapeit4</a> is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads using <a href="https://whatshap.readthedocs.io/en/latest/" rel="nofollow noreferrer">WhatsHap</a> first however. The guide for WhatsHap can be found <a href="https://whatshap.readthedocs.io/en/latest/guide.html" rel="nofollow noreferrer">here</a> and has some info on using data processed using GATK. </p>
  
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Answers.CreationDate: 2020-01-10T18:04:13.090Z
Answers.LastActivityDate: 2020-01-10T18:04:13.090Z
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Body: <p>I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account.  I've found <a href="https://academic.oup.com/bioinformatics/article/35/14/i242/5529122" rel="nofollow noreferrer">this paper</a> which sounds like what I am looking for, but that tool was developed specifically for Hi-C data, and I only have exomes.</p>
  
  <p>Thanks</p>
  
Tags: <exome><genetics><phasing>
Title: Read-informed statistical phasing
ThreadText: # Read-informed statistical phasing
  
  (Asked by: username_0 on 2020-01-06)
  
  I'm wondering if there are any tools out there that perform statistical phasing of genetic data (e.g. Eagle) that take read-based phasing from GATK into account. I've found [this paper](https://academic.oup.com/bioinformatics/article/35/14/i242/5529122) which sounds like what I am looking for, but that tool was developed specifically for Hi-C data, and I only have exomes.
  
  Thanks
  
  **Tags:** exome, genetics, phasing
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2020-01-10. Score: 1
  
  [shapeit4](https://odelaneau.github.io/shapeit4/) is currently (probably) the most accurate and quickest phasing algorithm which can account for sequencing reads in the model. They suggest you extract the phase information from the reads using [WhatsHap](https://whatshap.readthedocs.io/en/latest/) first however. The guide for WhatsHap can be found [here](https://whatshap.readthedocs.io/en/latest/guide.html) and has some info on using data processed using GATK.
  
  
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