FusionToolFilter

Filtering of Fusion Detection Tool Results using Spanning- & Junction Read Counts.

Usage:

filter_fusion_out.py [-h] -i INPUT -o OUTPUT
     -t {starfusion,fusioncatcher,jaffa,arriba}
     [--threshold-junction THRESHOLD_JUNCTION]
     [--threshold-spanning THRESHOLD_SPANNING]
     [--threshold-confidence {HighConfidence,MediumConfidence,LowConfidence}]
     [--fusion-inspector {yes,no}]

Filter output of either STAR-Fusion or fusionCatcher fusion gene detection tool.

Arguments:
     -h, --help show this help message and exit
     -i, --input Input file
     -o, --output Desired output file name
     -t, --tool {starfusion,fusioncatcher,jaffa,arriba} Select tool that generated output file
     --threshold-junction Amount of junction reads to filter by (only starfusion & arriba)
     --threshold-spanning Amount of spanning frag reads to filter by (only starfusion & arriba)
     --threshold-confidence {HighConfidence,MediumConfidence,LowConfidence} Confidence level to filter by (only jaffa)
     --fusion-inspector {yes,no} Additional filtered file with the first column formatted for FusionInspector

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Directory	Content
modules	Fusion Detection Tool methods
tests	Unittests