> For clean Markdown of any page, append .md to the page URL.
> For a complete documentation index, see https://docs.nvidia.com/clara/parabricks/llms.txt.
> For AI client integration (Claude Code, Cursor, etc.), connect to the MCP server at https://docs.nvidia.com/clara/parabricks/_mcp/server.

# starfusion

Identifies candidate fusion transcripts.

This tool performs fusion calling for RNA-Seq samples, utilizing the
STAR-Fusion algorithm. This requires input of a genome resource library, in
accordance with the original STAR-Fusion tool, and outputs candidate fusion
transcripts.

Refer to the [starfusion Reference](#options) section for a detailed listing of all available options.

## Quick Start

```sh
# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
    pbrun starfusion \
    --chimeric-junction /workdir/${CHIMERIC_JUNCTION_INPUT} \
    --genome-lib-dir /workdir/${PATH_TO_GENOME_LIBRARY}/ \
    --output-dir /outputdir/${PATH_TO_OUTPUT_DIRECTORY}/
```

## Compatible CPU Command

The command below is the CPU counterpart of the Parabricks command above. The output
from this command will be identical to the output from the above command.

```sh
$ ./STAR-Fusion \
    --chimeric_junction <INPUT_DIR>/${CHIMERIC_JUNCTION_INPUT} \
    --genome_lib_dir <INPUT_DIR>/${PATH_TO_GENOME_LIBRARY} \
    --output_dir <OUTPUT_DIR>/${PATH_TO_OUTPUT_DIRECTORY}
```

## Options