<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>

CC BY-SA 4.0
2023-11-23T14:13:11.057Z
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.
Community
CC BY-SA 4.0
2023-11-24T12:30:20.177Z
@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.
Lukas Chumchal
<variation>
Eigen phred score interpretation
# 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

