Table 1. Software tools evaluated for performance in detection of DSVs in WGS.
| Software tool | Primary SV detection methods employed | Chr 1 simulation | WGS simulation |
|---|---|---|---|
| Breakdancer | PEM | PASS | PASS |
| Clever | Read alignment graph and max cliques | PASS | |
| Cn.MOPS | DOC and Poisson distribution | ||
| Control-freec | SNP B allele frequencies and DOC | PASS | |
| Dindel | Realignment with probabilistic indel calls | ||
| ERDS | DOC and paired Hidden Markov Model | PASS | |
| GasvPRO | DOC, PEM and probabilistic model | ||
| GenomeStrip | DOC, PEM and SRM | PASS | PASS |
| Lumpy | PEM and DOC (SRM with special aligner) | PASS | |
| SVDetect | DOC, PEM |
Abbreviations: BD, breakdancer; DOC, depth of coverage; ERDS, estimation by read depth with single-nucleotide variants; GS, GenomeStrip; PEM, paired end mapping; SNP, single nucleotide polymorphism; SRM, split read mapping; TP, true positive; WGS, whole-genome sequence.