Flow Space Alternate Allele Calculation (FAO) calculation

Flow Space Alternate Allele Calculation (FAO) is calculated with the following formula.

Key for formula below

AF: Allele frequency

AO: Alternate allele depth at position

RO: Reference allele depth at position

DP: Total depth at position

FAO: Flow space alternate allele depth at position

FRO: Flow space reference allele depth at position

FDP: Flow total depth at position

1. FAO is usually equal to AO; however, due to complex alleles and/or downsampling*, FAO may differ from AO.

2. AF = FAO / (FAO + FRO) and not FAO / FDP. This is because FDP may include reads that do not fit the flow space profile of any hypothesis; in such cases, FDP ≥ FAO + FRO and this is not used in allele frequency calculation.

Exception: When flow correction is not performed and there are no F tags in the VCF file, then DP = AO + RO and AF = AO / DP.

*FAO along with all the F tags are subject to downsampling but AO/DP/RO/SAF/SAR/SRF/SRR are not. So when total coverage is higher than the downsampling cutoff, FAO tends to be smaller than AO.