Variant Allele Frequency from Ion Torrent data
Entering edit mode
6.6 years ago
stamakro ▴ 40

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?


snp sequencing vaf Ion Torrent • 3.7k views
Entering edit mode
6.6 years ago
Katie D'Aco ★ 1.0k

The fields FPD and FAO are after correcting for flow order of nucleotides, and so should be more accurate.

From it looks like they don't use FPD in their allele freq calculations:

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


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