Question: Calculate the b allele frequency from a VCF file
0
2.3 years ago by
Maj0
Maj0 wrote:

Hello,

I have to calculate the b-allele frequency from a vcf file. But I have some problems to understand some genotypes.

For example :

1/1:17:283,34,24:2,15:69,68

How can i calculate the BAF ? ( number of reads of the alternatif allele/ number of reads)

I don't know if 17/17 (=1) it's correct or not ?

And if the genotype is 0/0, the baf is equal to 0 ?

frequency vcf • 2.7k views
modified 2.3 years ago by jmzeng131490 • written 2.3 years ago by Maj0
1

What's the GT FORMAT? That information would help a lot in figuring out what the genotype value you've given us means.

1
2.3 years ago by
jmzeng131490
jmzeng131490 wrote:

The same question:Computing B-Allele Frequency From Bam Or Vcf Related To Exome Samples

as far as I can see , the AD = 2,15 , so the BAF=2/(2+15)

1

Indeed GT format would help. In this case: - 1/1: homozygous do ALT - AD: 2,15 . REF = 2 reads ; ALT = 15 reads

According to Computing B-Allele Frequency From Bam Or Vcf Related To Exome Samples BAF = coverage Alt / (coverage Alt + coverage Ref)

``````BAF = 15/(2+15) = 0.8823
``````