Body: <p>I need help. I am not able to find any reference for Eigen_phred_coding prediction tools score from <a href="http://database.liulab.science/dbNSFP" rel="nofollow noreferrer">dbNSFP</a>.</p>
  <p>I know that it may be scaled in a similar manner to CADD_phred - ranking raw values from highest to smallest; get rank of that value in the queue; phred scale that value with the same formula as sequencing quality score.</p>
  <p>But I couldn't find the phred scaling of Eigen values directly, not to mention its suggested cutoff (same as CADD_phred &gt; 15 or different?).</p>
  <p><strong>How are the Eigen scores transformed into Eigen_phred?</strong></p>
  <p><strong>Is it in same manner as Cadd_phred?</strong></p>
  <p><strong>If so, can same cutoff be used in both cases?</strong></p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-23T14:13:11.057Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-11-24T12:30:20.177Z
Comments.Text: @terdon Thank you for that reference. I don't know why, but I always thought that CADD_phred is phred scaled value of ratio rank of value in sorted queue over the total number of used SNV. At least in read me I found out that everything phred is  ratio of rank of the variat over total number of scores in database. Still I am not sure with the cutoff of 15. Anyway I am going to try that.
Comments.UserDisplayName: Lukas Chumchal
Tags: <variation>
Title: Eigen phred score interpretation
ThreadText: # Eigen phred score interpretation
  
  (Asked by: username_0 on 2023-11-23)
  
  I need help. I am not able to find any reference for Eigen\_phred\_coding prediction tools score from [dbNSFP](http://database.liulab.science/dbNSFP).
  
  I know that it may be scaled in a similar manner to CADD\_phred - ranking raw values from highest to smallest; get rank of that value in the queue; phred scale that value with the same formula as sequencing quality score.
  
  But I couldn't find the phred scaling of Eigen values directly, not to mention its suggested cutoff (same as CADD\_phred > 15 or different?).
  
  **How are the Eigen scores transformed into Eigen\_phred?**
  
  **Is it in same manner as Cadd\_phred?**
  
  **If so, can same cutoff be used in both cases?**
  
  **Tags:** variation
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  > **username_0**: @terdon Thank you for that reference. I don't know why, but I always thought that CADD_phred is phred scaled value of ratio rank of value in sorted queue over the total number of used SNV. At least in read me I found out that everything phred is  ratio of rank of the variat over total number of scores in database. Still I am not sure with the cutoff of 15. Anyway I am going to try that.  
  
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  ## 0 answers
  
  