To the best of our knowledge, Chimera is the only available software able to integrate and compare the data produced by different fusion detection tools.
Several considerations such as different nodule detection, tools and measurement assessments should be taken into account in order to avoid false-negative diagnoses as well as unnecessary follow-up examinations.
With the functions made available by Chimera, the user can import data from 11 different fusion detection tools, represented on top of Figure 1, into a list of fusions.
Summary: Chimera is a Bioconductor package that organizes, annotates, analyses and validates fusions reported by different fusion detection tools; current implementation can deal with output from bellerophontes, chimeraScan, deFuse, fusionCatcher, FusionFinder, FusionHunter, FusionMap, mapSplice, Rsubread, tophat-fusion and STAR.
Some explanations may be put forward to account for those discrepancies: the current study is multicentric, and the detection tools are different (PCR versus arrays with different targets for the same gene).
Comparing the agreement between tools with the same technique with different thresholds and the agreement between tools with different detection techniques, we observed that the latter is lower, but not significantly.
Different tools implement different detection techniques and sometimes the same technique can be implemented with variations specific to a particular tool, such as different threshold values.
We will also apply software analysis and vulnerability detection tools in different scenarios.
We have also examined these sSNV detection tools at different allele frequencies using simulation data.
