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Table 2 Inversion prediction in individual NA12878

From: An integrative probabilistic model for identification of structural variation in sequencing data

Method Minimum number to detect 1 Minimum number to detect 2 Minimum number to detect 3
High quality alignments    
   Breakdancer 47 (37) 80 (221) NA (NA)
   GASV 34 (158) 76 (298) 5,028 (NA)
   GASVPro-HQ 11 (20) 116 (102) 206 (346)
   Hydra-HQ 61 (139) 108 (246) 284 (NA)
All alignments    
   GASVPro 28 (59) 394 (286) 550 (504)
   GASVPro-Min2 28 (59) 160 (334) NA (NA)
   Hydra 159 (258) NA (470) NA (NA)
  1. We report the results on both Pilot 2 and Pilot 1, with the Pilot 1 results in parentheses. In most cases the sensitivity of inversion detection increases with coverage with more methods correctly predicting three inversions in the higher coverage Pilot 2 data. In some cases, true inversions identified by the uniquely mapped data are lost with the addition of ambiguous alignments. These alignments result in substantially more predictions, which can cause true inversions to be eliminated in the pruning process. The benefit of our probabilistic method and inclusion of the beRD signal is evident as higher specificity is attained by GASVPro and GASVPro-HQ compared to GASV, when predicting the top inversion. NA, not applicable.