arriba
Tool for the detection of gene fusions from RNA-Seq data.
$ pbrun arriba \
--ref reference.fasta \
--in-bam input.bam \
--in-gene-annotation geneAnnotations.gtf \
--out-fusions-file passingFusions.tsv \
--out-filtered-fusions-file discardedFusions.tsv
Detect gene fusions from RNA-Seq data.
Input/Output file options
- --in-bam IN_BAM
- --ref REF
- --in-gene-annotation IN_GENE_ANNOTATION
- --in-blacklist-file IN_BLACKLIST_FILE
- --in-known-fusions-file IN_KNOWN_FUSIONS_FILE
- --in-fusions-tag-file IN_FUSIONS_TAG_FILE
- --in-protein-file IN_PROTEIN_FILE
- --out-fusions-file OUT_FUSIONS_FILE
- --out-filtered-fusions-file OUT_FILTERED_FUSIONS_FILE
Path to the input BAM file (default: None)
Option is required.
FastA file with genome sequence(assembly) (default: None)
Option is required.
GTF file with gene annotation. The file may be gzip-compressed (default: None)
Option is required.
File containing blacklisted ranges (default: None)
File containing known/recurrent fusions (default: None)
Tab-separated file containing fusions to annotate with tags in the tags column (default: None)
File in GFF3 format containing coordinates of the protein domains of genes (default: None)
Output file with fusions that have passed all filters (default: None)
Option is required.
Output file with fusions that were discarded due to filtering. (default: None)
Options specific to this tool
(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.