Structural Variants: Why Finding One, Placing It, and Genotyping It Are Three Different Problems

For a SNV, "detected" and "characterized" are nearly the same thing. An SV call is a composite claim: an event of some type exists, spanning roughly this interval, with breakpoints here, in this many copies. A pipeline can be right about the first part and wrong about the rest — and the standard F1 score won't distinguish those cases, because SV benchmarking counts a call correct when it lands within a tolerance window. In multi-sample data, genotypers whose detection F1 spanned 0.605 to 0.948 had genotype concordance ranging from 33.8% to 84.9%. Report all three properties, not one.