This is my first time using FreeBayes on Galaxy. Does anyone know how to calculate the variant allele frequency (some call it alternate allele frequency) from the VCF? Some headers that I think would apply are:
##FORMAT=<ID=AD,Number=R,Type=Integer,Description=“Number of observation for each allele”>
##FORMAT=<ID=RO,Number=1,Type=Integer,Description=“Reference allele observation count”>
##FORMAT=<ID=AO,Number=A,Type=Integer,Description=“Alternate allele observation count”>
I was thinking maybe AO/DP?
Another question I had was, there is an option for pre-calculated variant allele frequency (see below for “AF”), but the VAF is always either 1.0 or 0.5. This seems suspicious because VAF are never that clean in the real world. Anyone have ideas why it does this?
##INFO=<ID=AF,Number=A,Type=Float,Description=“Estimated allele frequency in the range (0,1]”>