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Table 2 Comparison of software performance in intra-individual InDel detection

From: DiSNPindel: improved intra-individual SNP and InDel detection in direct amplicon sequencing of a diploid

Softwarea

True InDels (%)

Size-correct InDels with wrong bases (%)

Missed InDels (%)

False positive InDels (%)

DiSNPindel

43(53.1 %)

20 (24.7 %)

18 (22.2 %)

0 (0.0 %)

novoSNP

6 (7.4 %)

7 (8.6 %)

68 (84.0 %)

34 (72.3 %)

Mutation surveyor

7 (8.6 %)

7 (8.6 %)

67 (82.8 %)

26 (65.0 %)

PrimeIndel

15 (18.5 %)

10 (12.3 %)

56 (69.1 %)

0 (0.0 %)

  1. The numbers of true, size-correct but base-wrong, missed and false positive InDels were detected with 77 single traces containing SSR-associated InDels [23]. More data were given in Additional file 3: Table S3
  2. aPolyPhred did not detect any InDels and was thus excluded from the comparison