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Table 1 Results of SV detection obtained by BreakDancer, MoDIL, CLEVER, CNVnator, and Pindel

From: ChopSticks: High-resolution analysis of homozygous deletions by exploiting concordant read pairs

  Depth of coverage
SV caller 2 5 10 15 20
BreakDancer 259/260 426/427 453/456 455/458 455/458
MoDIL 1/1 27/27 96/96 129/130 –/–
CLEVER 398/462 449/525 454/491 454/478 454/466
CNVnator 326/1,258 354/952 422/1,127 447/1,211 451/1,258
Pindel 85/85 317/317 436/438 450/454 456/456
  1. Results of deletion calls by BreakDancer, MoDIL, CLEVER, CNVnator, and Pindel. The values to the left of ”/” are the numbers of correct deletion calls, where a correct deletion call is the one that overlaps with exactly one true deletion, which, in turn, only overlaps with the deletion call; the values to the right of ”/” are the numbers of all deletion calls. BreakDancer and CLEVER results were good in both sensitivity and specificity. CNVnator generated numerous false positives, while Pindel suffered from low coverage. MoDIL missed lots of deletions.