Skip to main content


Table 1 Summary of SV detection tools.

From: iSVP: an integrated structural variant calling pipeline from high-throughput sequencing data

Tool Algorithm Detectable SV types Simulation 30× CPU time, max. memory size NA12878 45× CPU time, max. memory size
BD RP DEL, INS, INV, TRA 1.6h, 0.3Gb 2.1h, 0.5Gb
Delly RP, RD, SR DEL, INV, DUP, TRA 1.3h, 0.5Gb 24h, 9Gb
Pindel SR DEL, INS, INV, DUP, TRA 19h, 3Gb 37h, 3Gb
HC AS DEL, INS, other 68h, *9Gb 180h, *9Gb
  1. SV detection tools are summarized according to algorithm types, detectable SV types, and computational resources required in our analyses. For each tool, CPU time and maximum memory size were measured for the 30× simulation data and the 45× whole genome sequence data of NA12878. RP, RD, SR, and RP stand for read pair, read depth, split read, and assembly approaches, respectively. 'BD' is BreakDancer. HC, Haplotype Caller; 'DEL', deletion; 'INS', insertion; 'INV', inversion; 'DUP', duplication; 'TRA', translocation.
  2. * HC was performed with explicitly specified maximum memory size.