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Table 2 Software versions used

From: Strategies for identification of somatic variants using the Ion Torrent deep targeted sequencing platform

Software Label Version Notes
Ion Reporter IR IonReporter Version 0.1.2 IonReporter VCF employs TVC 4.2
Poorman’s PM Torrent Variant Caller 4.2 Subtract variants found in normal
Varscan VS varscan2.3.5 reject p-value p>10−6
MuTect MU muTect-1.1.7.jar  
MuTect-Gaps MG muTect-1.1.7.jar nearby_gap_events added (see “Results” section)
  1. Unmodified MuTect (MU) was not used in the analyses described because it produced so few variants