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Table 1 Variant loci counts from each tool

From: A genome-wide survey of mutations in the Jurkat cell line

  GATK Pindel Breakdancer CNVnator Merged
Substitutions 3,520,988     3,520,988
Short Hom. Deletion 170,397     170,397
Short Deletion 841,001 1,239,299 47   1,460,321
  (70%) (47%) (0%)   
Short Insertion 326,446 616,298    729,727
  (65%) (35%)    
Long Hom. Deletion 326    108 434
  (0%)    (0%)  
Long Deletion 1904 118,610 6081 2499 125,397
  (61%) (1.4%) (10%) (1.2%)  
Long Insertion 1039 125,918 18   126,657
  (31%) (0.25%) (0%)   
Duplication   17,762   1863 15,288
   (22%)   (24%)  
Inversion   149,545 183   149,715
   (0.0087%) (7.1%)   
Intra. Translocation    1981   1981
Inter. Translocation   4 113   117
   (0%) (0%)   
  1. The percentage of sites that overlap the other tools is provided where applicable