> This page is for version v4.8.0 (default).
> For other versions, use one of these documentation indexes:
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> - v4.7.1: https://docs.nvidia.com/clara/parabricks/v4.7.1/llms.txt

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# 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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.8.0-1 \
    pbrun starfusion \
    --chimeric-junction /workdir/${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

| Type        | Name                                    | Required? | Description                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| ----------- | --------------------------------------- | --------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
| I/O         | `--chimeric-junction CHIMERIC_JUNCTION` | Yes       | Path to the Chimeric.out.junction file produced by STAR.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    |
| I/O         | `--genome-lib-dir GENOME_LIB_DIR`       | Yes       | Path to a genome resource library directory. For more information, visit [https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion#data-resources-required](https://github.com/STAR-Fusion/STAR-Fusion/wiki/installing-star-fusion#data-resources-required).                                                                                                                                                                                                                                                                                  |
| I/O         | `--output-dir OUTPUT_DIR`               | Yes       | Path to the directory that will contain all of the generated files.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| Tool        | `--out-prefix OUT_PREFIX`               | No        | Prefix filename for output data.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            |
| Performance | `--num-threads NUM_THREADS`             | No        | Number of threads for worker. (default: 4)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  |
| Runtime     | `--verbose`                             | No        | Enable verbose output.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime     | `--x3`                                  | No        | Show full command line arguments.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           |
| Runtime     | `--dry-run`                             | No        | Check if the current command is valid.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |
| Runtime     | `--logfile LOGFILE`                     | No        | Path to the log file. If not specified, messages will only be written to the standard error output.                                                                                                                                                                                                                                                                                                                                                                                                                                                         |
| Runtime     | `--tmp-dir TMP_DIR`                     | No        | Full path to the directory where temporary files will be stored. (default: .)                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |
| Runtime     | `--with-petagene-dir WITH_PETAGENE_DIR` | No        | Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials. Optionally set the PetaLinkMode environment variable that is used to further configure PetaLink, notably setting it to "+write" to enable outputting compressed BAM and .fastq files. |
| Runtime     | `--keep-tmp`                            | No        | Do not delete the directory storing temporary files after completion.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Runtime     | `--no-seccomp-override`                 | No        | Do not override seccomp options for docker.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 |
| Runtime     | `--version`                             | No        | View compatible software versions.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          |
| Runtime     | `--preserve-file-symlinks`              | No        | Override default behavior to keep file symlinks intact and *not* resolve the symlink.                                                                                                                                                                                                                                                                                                                                                                                                                                                                       |
| Runtime     | `--help-json`                           | No        | Print out help message in JSON format.                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      |