Entering edit mode

3.5 years ago

DareDevil
★
4.3k

How is allelle frequency calculated ?

This a variation where Allelle Frequency (AF) is 0.500 and AD = 57,36 and DP = 93

My understanding about AF calculation is `36 / 93 = 0.387096774`

```
chr1 976215 rs7417106 A G 687.60 . AC=1;AF=0.500;AN=2;BaseQRankSum=0.978;DB;DP=93;ExcessHet=3.0103;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.000;QD=7.39;ReadPosRankSum=1.018;SOR=0.666 GT:AD:DP:GQ:PL 0/1:57,36:93:99:695,0,1225
```

@Pierre Lindenbaum Thanks for the quick reply!!.

But if you look at this post, they mention about

`AD`

and`DP`

for calculating`AF`

and what is the conclusion of the post you mentioned ?

there is no precised conclusion there. But if you look at these following post here and here. They mention about relating AD and DP in calculating varint allelle frequncy

add VAF or FREQ in vcf file from read depth and Calculation of VAF (variant allele frequency) are about

VARIANT allele frequencyNOT **allele frequency'Thanks.. Little confused with the terms