Hi Biostars Leaders,

Freebayes(version:v1.0.1-1-g683b3cc-dirty) defines AF as Description="Estimated allele frequency in the range (0,1]", but the values are always either 0.5 or 1.0, and they are not actual observed frequencies.

I have observed the same with GATK's HaplotypeCaller, and I have custom calculated the actual frequencies from Ref & Alt Alleles i.e. from the AD field.

Freebayes does not spit out the AD field, but it has these following fields which I think I can use : 
RO = "Reference allele observation count, with partial observations recorded fractionally"
AO = "Alternate allele observations, with partial observations recorded fractionally"
 
I am wondering if there is any advice on how to calculate actual allele frequencies for Freebayes ?

thanks,
gsr
I got answer to my own question.

I just installed a newer version of freebayes (v1.1.0-3-g961e5f3-dirty) which does spit out the AD field "Number of observation for each allele"

I then used the AD field to calculate the actual allele frequencies in human sample(NA12878)