Examples of equivalent, but differently annotated variants. (A) When several nearby bases are changed, this can be described as one large substitution or as several smaller ones, even though the resulting sequence is the same. (B) Variant was present, but changes were described as part of a larger variant. (C) Canonicalization issues: Variants can often be described at various different positions, and variants originating from different sources may use different conventions, which must be taken into account during comparisons. (D) In the VCF format, overlapping variants can result in a different description of variants than had they occurred in isolation, a subtlety not always dealt with correctly in comparison algorithms.
