Basis of comparison | Region overlap (Additional file 1: Figure S2a) | Breakpoint closeness (Additional file 1: Figure S2b) |
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Description | SVs match if there is sufficient overlap, determined with a Jaccard threshold parameter, between the genomic region associated with the called SV and that of the known SV | SVs match if the breakpoints of the called SV are sufficiently close to the those of the known SV, i.e. breakpoints are within f bp of one another where f is a flank parameter |
Strengths | ● Identifies genomic regions affected by the known SVs | ● Suited to all types of SVs ● Evaluates precision of breakpoint predictions, facilitating subsequent breakpoint validation |
Weaknesses | ● Some SVs are not accurately defined by genomic regions, e.g., an insertion may be characterized by a single breakpoint ● Need criteria to define sufficient overlap | ● Need criteria to define sufficient closeness |