text: user3004: I am working on ION Torrent S5 XL and I am facing to an issue with VCF output generated by the variant caller of thermofisher. It stating on VCF 4.1 that Phred Quality Score is on a range of 0 to 255. In my VCF I have values over than 255. Do you know if there is a way to transform these values?
  
  user181: See this post on the GATK forums.
  It is normal to see values above 255.  The QUAL score is the posterior probability that all samples in your callset are homozygous reference. I quote Sheila's response from the thread posted above:
  
  The QUAL score is the Phred-scaled posterior of AC = 0. We use the AC priors and the PLs to get the likelihood of the data given each AC, then use those to get the posterior probability for each AC. From there, the calculation is 1 - Pr{AC > 0}.
  
  Please see the GATK post in Methods and Algorithms for the nitty gritty details. Beware, Bayesian statistics abound.
  
original_text: 3004: <p>I am working on ION Torrent S5 XL and I am facing to an issue with VCF output generated by the variant caller of thermofisher. It stating on VCF 4.1 that Phred Quality Score is on a range of 0 to 255. In my VCF I have values over than 255. Do you know if there is a way to transform these values?</p>
   181: <p>See <a href="https://gatkforums.broadinstitute.org/gatk/discussion/2403/gatks-quality-scores-on-vcf-files" rel="nofollow noreferrer">this post</a> on the GATK forums.</p>
  
  <p>It is normal to see values above 255.  The QUAL score is the posterior probability that all samples in your callset are homozygous reference. I quote Sheila's response from the thread posted above:</p>
  
  <blockquote>
    <p>The QUAL score is the Phred-scaled posterior of AC = 0. We use the AC priors and the PLs to get the likelihood of the data given each AC, then use those to get the posterior probability for each AC. From there, the calculation is 1 - Pr{AC > 0}.</p>
  </blockquote>
  
  <p>Please see the GATK post in Methods and Algorithms for the <a href="https://software.broadinstitute.org/gatk/documentation/article.php?id=7258" rel="nofollow noreferrer">nitty gritty details</a>. Beware, Bayesian statistics abound.</p>
  