starfusion

Identifies candidate fusion transcripts.

Quick Start

$ pbrun starfusion \
    --chimeric-junction sample_x.out.junction \
    --genome-lib-dir HG38 \
    --output-dir sample_X/

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.

$ ./STAR-Fusion --chimeric_junction sample_x.out.junction --genome_lib_dir HG38 --output_dir sample_X/

starfusion Reference

Identify candidate fusion transcripts supported by Illumina reads.

Input/Output file options

--chimeric-junction CHIMERIC_JUNCTION

Path to the Chimeric.out.junction file produced by STAR. (default: None)

Option is required.

--genome-lib-dir GENOME_LIB_DIR

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.

--output-dir OUTPUT_DIR

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

Number of threads for worker. (default: 4)

--out-prefix OUT_PREFIX

Prefix filename for output data. (default: None)

Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

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)

--keep-tmp

Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.

--no-seccomp-override

Do not override seccomp options for docker (default: None).

--version

View compatible software versions.