Filtering of Fusion Detection Tool Results using Spanning- & Junction Read Counts.
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
| Directory | Content |
|---|---|
| modules | Fusion Detection Tool methods |
| tests | Unittests |