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Table 2 Performance of different general indel annotation programs

From: Comparative assessments of indel annotations in healthy and cancer genomes with next-generation sequencing data

Tool

TP indels

FP indels

Recall

Precision

F

Varscan

533,101

424,740

0.42

0.56

0.48

GATK_UG

884,763

1,802,477

0.69

0.33

0.45

GATK_HC

948,738

2,026,903

0.74

0.32

0.45

Pindel

446,622

619,846

0.35

0.42

0.38

Dindel

994,947

3,097,117

0.78

0.24

0.37

Platypus

941,046

3,403,565

0.74

0.22

0.33

SAMTools

930,860

15,083,658

0.73

0.06

0.11

  1. The bold represents the highest value in each column
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BMC Medical Genomics

ISSN: 1755-8794

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