I have a vcf file with SNPs called using the Torrent Variant Caller and I want to calculate their Variant Allele Frequencies.
The issue is that there is both a DP (depth) and a FPD (flow depth) fields as well as an AO (Alternate Allele Observations) and a FAO (Flow Alternate Allele Observations) fields and the two often disagree by a lot.
Which pair should I trust? DP & AO or FDP & FAO?
Or should I just ignore the cases where they disagree?