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usage.md

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Running the tool

Before running the tool make sure you have downloaded all the necessary resources!

Run all fusion detection tools

fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
  --arriba tests/test_data/arriba.tsv \
  --ericscript tests/test_data/ericscript.tsv \
  --starfusion tests/test_data/starfusion.tsv \
  --fusioncatcher tests/test_data/fusioncatcher.txt \
  --squid tests/test_data/squid.txt \
  --pizzly tests/test_data/pizzly.tsv \
  --dragen tests/test_data/dragen.tsv \
  --jaffa tests/test_data/jaffa.csv \
  --allow-multiple-gene-symbols

Multiple gene symbols

In case fusion gene symbol can't be uniquely determined some tools provide possible list of fusions. Each fusion tool handles this differently. There are two options:

Example case

Dummy fusion detected by Squid: 15 34347968 34348134 19 15254151 15254264 . 9 - - fusion-gene BRD4:NUTM1,BRD4-1:NUTM1.

  1. Omitting --allow-multiple-gene-symbols will report only first fusion: BRD4:NUTM1.
  2. Adding --allow-multiple-gene-symbols will treat each fusion as unique and report BRD4:NUTM1 and BRD4-1:NUTM1.

Set a custom weight for tool

Each tool has a predefined weight when estimating score of a fusion. On default all tools have an equal weight (100 / NUMBER_OF_RUNNING_TOOLS). To change the weights follow the steps below:

fusion_report run "<SAMPLE NAME>" /path/to/output /path/to/db/ \
  --ericscript tests/test_data/ericscript.tsv \
  --ericscript_weight 30.5 \
  --fusioncatcher tests/test_data/fusioncatcher.txt \
  --fusioncatcher_weight 70.5

All parameters and options

fusion_report --help
fusion_report run --help
fusion_report download --help
fusion_report sync --help