Continuous AF with GATK

[matan8]

Hi,
I saw some VCF files that have a continuous AF value. In my results the AF values are either 1 or 0.5.
I am working on yeast, so the sequencing was done on several different DNA and the AF value is my way to decide whether it is a real mutation or not.

[vivek_]

The AF value in the VCF files should be a per sample frequency. How many samples do you have in the VCF?

[matan8]

Only one sample in each file, but I don't understand the relevance.
I thought that the AF value should be refCount/depth or something like that...

[vivek_]

From the 1000 gneomes website:

The vcf files can also provide information like allele frequency for the variants. The allele frequency is given in the info column of the vcf file with the key AF. This frequency will be based on all the individuals/populations in the file unless otherwise documented

I think its just for the alleles called by the genotyper. So if your sample is het, the AF is 0.5 and if its homozygous alternate its 1.0