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.
See the starfusion Reference section for a detailed listing of all available options.
# 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 $(pwd):/outputdir \
--workdir /workdir \
nvcr.io/nvidia/clara/clara-parabricks:4.7.0-1 \
pbrun starfusion \
--chimeric-junction /workdir/${CHIMERIC_JUNCTION_INPUT} \
--genome-lib-dir /workdir/${PATH_TO_GENOME_LIBRARY}/ \
--output-dir /outputdir/${PATH_TO_OUTPUT_DIRECTORY}/
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.
$ ./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}
Identify candidate fusion transcripts supported by Illumina reads.
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. |
| 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 | --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. |