Identifies candidate fusion transcripts.
$ pbrun starfusion \
--chimeric-junction sample_x.out.junction \
--genome-lib-dir HG38 \
--output-dir sample_X/
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 sample_x.out.junction --genome_lib_dir HG38 --output_dir sample_X/
Identify candidate fusion transcripts supported by Illumina reads.
Input/Output file options
- --chimeric-junction CHIMERIC_JUNCTION
- --genome-lib-dir GENOME_LIB_DIR
- --output-dir OUTPUT_DIR
Path to the Chimeric.out.junction file produced by STAR. (default: None)
Option is required.
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. (default: None)
Option is required.
Path to the directory that will contain all of the generated files. (default: None)
Option is required.
Options specific to this tool
- --num-threads NUM_THREADS
- --out-prefix OUT_PREFIX
Number of threads for worker. (default: 4)
Prefix filename for output data. (default: None)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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 (default: None)
Do not delete the directory storing temporary files after completion.
Path to license file license.bin if not in the installation directory.
Do not override seccomp options for docker (default: None).
View compatible software versions.