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 ?