Variant Equivalence

A common problem in calling genomic variation is the multitude of ways a variation can be annotated. Two different variant callers might describe the same genomic alternations in two different ways. For example, consider the variation that occurs in the figure below: either notation captures the event correctly, but one considers there to be an SNV then insertion while the other considers the event a deletion and subsequent insertion. These differences make comparisons across data sets more difficult. To alleviate the problem, there are standards emerging that tools can adhere to and software to help normalize notation of variants, but the problem still exists.