starfusion - NVIDIA Docs

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.

Quick Start

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            # 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 $(pwd):/outputdir \
    --workdir /workdir \
    nvcr.io/nvidia/clara/clara-parabricks:4.5.1-1 \
    pbrun starfusion \
    --chimeric-junction /workdir/${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.

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            $ ./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}

starfusion Reference

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.