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Table 1 Caller scoring schemes

From: Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection

Basis of comparison

Region overlap

(Additional file 1: Figure S2a)

Breakpoint closeness

(Additional file 1: Figure S2b)

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