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
AD = 2,15
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 ?
Thanks for advance
•
written
by
Maj •
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)
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
Log in to answer this question.
What's the GT FORMAT? That information would help a lot in figuring out what the genotype value you've given us means.