text: user59: 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 which sounds like what I am looking for, but that tool was developed specifically for Hi-C data, and I only have exomes.
  Thanks
  
  user3694: 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 first however. The guide for WhatsHap can be found here and has some info on using data processed using GATK. 
  
original_text: 59: <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>
   3694: <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>
  