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Table 2 Validation of deletion callings from NA12878 data.

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

Tool

Called (≥50 bp)

Mills (n= 79)

Conrad (n= 351)

Kidd (n= 58)

BD

5,014

13

158

49

Delly

286,289

13

168

51

Pindel

7,265

28

143

33

HC

1,880

4

0

0

iSVP

8,130

30

166

49

  1. The sensitivity of deletion calling for each tool was confirmed by comparing to multiple datasets from the literature (Mills [25], Conrad [23], and Kidd [24]). The n in parentheses shows the number of total validated deletions for each experiment. BD and HC stand for BreakDancer and Haplotype Caller, respectively.