Tool ReferenceTools

starfusion

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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 section for a detailed listing of all available options.

Quick Start

1# This command assumes all the inputs are in the current working directory and all the outputs go to the same place.
2docker run --rm --gpus all --volume $(pwd):/workdir --volume $(pwd):/outputdir \
3    --workdir /workdir \
4    nvcr.io/nvidia/clara/clara-parabricks:4.7.1-1 \
5    pbrun starfusion \
6    --chimeric-junction /workdir/${CHIMERIC_JUNCTION_INPUT} \
7    --genome-lib-dir /workdir/${PATH_TO_GENOME_LIBRARY}/ \
8    --output-dir /outputdir/${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.

1$ ./STAR-Fusion \
2    --chimeric_junction <INPUT_DIR>/${CHIMERIC_JUNCTION_INPUT} \
3    --genome_lib_dir <INPUT_DIR>/${PATH_TO_GENOME_LIBRARY} \
4    --output_dir <OUTPUT_DIR>/${PATH_TO_OUTPUT_DIRECTORY}

Options

TypeNameRequired?Description
I/O--chimeric-junction CHIMERIC_JUNCTIONYesPath to the Chimeric.out.junction file produced by STAR.
I/O--genome-lib-dir GENOME_LIB_DIRYesPath 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_DIRYesPath to the directory that will contain all of the generated files.
Tool--out-prefix OUT_PREFIXNoPrefix filename for output data.
Performance--num-threads NUM_THREADSNoNumber of threads for worker. (default: 4)
Runtime--verboseNoEnable verbose output.
Runtime--x3NoShow full command line arguments.
Runtime--logfile LOGFILENoPath to the log file. If not specified, messages will only be written to the standard error output.
Runtime--tmp-dir TMP_DIRNoFull path to the directory where temporary files will be stored. (default: .)
Runtime--with-petagene-dir WITH_PETAGENE_DIRNoFull 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-tmpNoDo not delete the directory storing temporary files after completion.
Runtime--no-seccomp-overrideNoDo not override seccomp options for docker.
Runtime--versionNoView compatible software versions.
Runtime--preserve-file-symlinksNoOverride default behavior to keep file symlinks intact and *not* resolve the symlink.