Locus View versus Allele View of variants

When you set workflow parameters, you can set the view that is used for variants in analysis results. The options for this setting are variants per position, Locus View, or variants per allele, Allele View. For more information on how to set this view, see Customize tuning parameters. The VCF files for both the Locus View and Allele View include one line for each variant row that is displayed in the Ion Reporter™ Software Analysis Results table.

The FDP (Flow Evaluator read depth at the locus) and DP (Total read depth at the locus) are subfields inside the INFO field of the VCF file. The values of these two fields remain the same for both the Locus View VCF file and the Allele View VCF file. These two fields, FDP and DP, are based on the TOTAL SUM of ALL the FAO (Flow Evaluator Alternate allele observations) and AO (Alternate allele observations) fields, which are based on the following formulas:

FDP=SUM(FAO)+FRO or DP=SUM(AO)+RO

Note: In Ion Reporter™ Software, the Allele View VCF file includes values of the FDP and DP fields that remain the same, although each allele is displayed as a single line of record in the Allele View VCF file.