What are the "Flow Evaluator" measures in the Ion Torrent Suite

[kgulukota]

I am looking at some VCF and bam files generated by Torrent Suite software onboard an Ion Torrent machine (PGM, if that matters).

The VCF has field pairs like the following:

• DP - Read Depth
• FDP - Flow evaluator read depth

There are similar "Flow Evaluator" counterparts for measures like Alternate Allele (AA) Observation Count, AA on fwd strand, AA on rev strand, Reference Allele (RA) observation, RA on fwd, RA on rev strand etc etc.

I looked on the web for what the Flow Evaluator measures refer to - but could not find much that is useful. Could someone elaborate? What is the significance of "Flow Evaluator" measures on the Ion Torrent platform? What is their definition? How should one interpret them when looking at called variants?

[kgulukota]

OK. I figured it out - posting here for the benefit of others who may be in the same predicament.

In the first step, FreeBayes is used to call variants based on sequence called by the basecaller routine.

Next, in the evaluation step, genomic variants called are compared to "flow space" readings. Specifically, the predicted flow space readings for three different hypothetical models are compared to the actual observed readings. The three models are: (1) reference allele, (2) alternate allele called by FreeBayes and (3) the original base call. Based on which hypothesis best fits, adjustments are made to base calls. The new, corrected base calls are used to calculate the "Flow Evaluator" metrics.

BTW, the flow space readings are included in the bam file in the ZM field.