<p>If you just have a VEP output (i.e. VCF) without raw genotypes then you cannot calculate the allelic fraction.</p>

CC BY-SA 4.0
2023-06-06T15:29:29.703Z
thanks user438383, how can calculate it if i have the vcf file?
Joman
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2023-06-06T16:04:02.540Z
@Joman See: https://www.biostars.org/p/147443/
Ram RS
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2023-06-06T15:12:50.017Z
2023-06-06T21:28:03.273Z
2023-06-06T21:28:03.273Z
user438383
<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>

CC BY-SA 4.0
2023-06-06T14:58:47.873Z
Please show a) your VEP output and b) describe what variant allelic fraction  means. Thank you.
user438383
<python><biopython><vep>
How to calculate the variant allelic fraction (VAF) from VEP output?
# 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.  

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## 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 user438383, how can calculate it if i have the vcf file?  
> **username_2**: @Joman See: https://www.biostars.org/p/147443/  

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