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Table 1 Comparison of SAMtools, PINDEL, PRISM and indelMINER on simulated dataset with 3,723 deletions and 3,777 insertions

From: Identification of indels in next-generation sequencing data

SV caller Observed indels False-positives False-negatives
SAMtools 6,491 172 (2.65%) 1181
PINDEL 7,239 328 (4.53%) 589
PRISM 7,406 301 (4.06%) 395
indelMINER 7,365 263 (3.57%) 398