Answers.Body: <p>If you just have a VEP output (i.e. VCF) without raw genotypes then you cannot calculate the allelic fraction.</p>
  
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Answers.CreationDate: 2023-06-06T15:29:29.703Z
Answers.Text: thanks user438383, how can calculate it if i have the vcf file?
Answers.UserDisplayName: Joman
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Answers.CreationDate: 2023-06-06T16:04:02.540Z
Answers.Text: @Joman See: https://www.biostars.org/p/147443/
Answers.UserDisplayName: Ram RS
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Answers.CreationDate: 2023-06-06T15:12:50.017Z
Answers.LastActivityDate: 2023-06-06T21:28:03.273Z
Answers.LastEditDate: 2023-06-06T21:28:03.273Z
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Body: <p><em>This question was also asked on <a href="https://www.biostars.org/p/9565421/" rel="nofollow noreferrer">Biostars</a></em></p>
  <p>How can I calculate the variant allelic fraction from the VEP file for multiple human samples?</p>
  <p>I used the ensembl-vep and it is human data.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-06-06T14:58:47.873Z
Comments.Text: Please show a) your VEP output and b) describe what variant allelic fraction  means. Thank you.
Comments.UserDisplayName: user438383
Tags: <python><biopython><vep>
Title: How to calculate the variant allelic fraction (VAF) from VEP output?
ThreadText: # How to calculate the variant allelic fraction (VAF) from VEP output?
  
  (Asked by: username_0 on 2023-06-06)
  
  *This question was also asked on [Biostars](https://www.biostars.org/p/9565421/)*
  
  How can I calculate the variant allelic fraction from the VEP file for multiple human samples?
  
  I used the ensembl-vep and it is human data.
  
  **Tags:** python, biopython, vep
  
  > **Comments:**
  > **username_1**: Please show a) your VEP output and b) describe what variant allelic fraction  means. Thank you.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-06-06. Score: 2
  
  If you just have a VEP output (i.e. VCF) without raw genotypes then you cannot calculate the allelic fraction.
  
  > **Comments:**
  > **username_0**: thanks username_1, how can calculate it if i have the vcf file?  
  > **username_2**: @username_0 See: https://www.biostars.org/p/147443/  
  
  ---
  
  