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

BMC Bioinformatics

Table 2 Software versions used

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)

Unmodified MuTect (MU) was not used in the analyses described because it produced so few variants

ISSN: 1471-2105