Truth datasets may consist of the following parts:
- a VCF file that provides variant calls
- a BED file to give confident regions. Typically, false-positive calls will be counted only in a subset of these regions.
The format of these files can vary depending on the benchmark type, e.g. for
diploid genotype comparisons, we require the GT format field to be present.
Note that "Confident Call Regions" from Truth and/or Query are applied only after the VCF comparison to enable better comparison of variants that can have different representations putting them either inside or outside the confident call regions. In contrast, if only variants inside the confident call regions are included during the VCF comparison, then some TP calls are incorrectly classified as FPs and/or FNs.
The query data consists of a single (g)VCF file.