**520**wrote:

Hi all,

So, I am interested in computing the VAF (variant allele frequency) by extracting values from a VCF file. From my understanding, the VAF is calculated as follows: AD(second entry)/DP so e.g.

```
AD = 8,4
DP = 12
VAF = 4/12
AD = 5,10
DP = 15
VAF = 10/15
```

Is this correct?

However, I've seen that sometimes the frequency of the most frequent (or less frequent) allele is computed. Hence it would be 8/12 and 10/15 (or 4/12 and 5/15 for the less frequent allele).

Or is this the difference between the AF (allele frequency), MAF (minor allele frequency) and VAF (variant allele frequency)? (also see MAF vs VAF on this topic)

And what about the 1/2 SNPs? do I have two values for VAF then?

```
AD = 0,5,10
DP = 15
VAF1 = 5/15
VAF2 = 10/15
```

I am slightly confused here. Thanks for your input!

**1.8k**• written 19 months ago by JJ •

**520**