arriba

Tool for the detection of gene fusions from RNA-Seq data.

Quick Start

$ 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

arriba Reference

Tool for the detection of gene fusions from RNA-Seq data

Input/Output file options

--in-bam IN_BAM

Path to the input bam file (default: None)

Option is required.

--ref REF

FastA file with genome sequence(assembly) (default: None)

Option is required.

--in-gene-annotation IN_GENE_ANNOTATION

GTF file with gene annotation. The file may be gzip-compressed (default: None)

Option is required.

--in-blacklist-file IN_BLACKLIST_FILE

File containing blacklisted ranges (default: None)

--in-known-fusions-file IN_KNOWN_FUSIONS_FILE

File containing known/recurrent fusions (default: None)

--in-fusions-tag-file IN_FUSIONS_TAG_FILE

Tab-separated file containing fusions to annotate with tags in the tags column (default: None)

--in-protein-file IN_PROTEIN_FILE

File in GFF3 format containing coordinates of the protein domains of genes (default: None)

--out-fusions-file OUT_FUSIONS_FILE

Output file with fusions that have passed all filters (default: None)

Option is required.

--out-filtered-fusions-file OUT_FILTERED_FUSIONS_FILE

Output file with fusions that were discarded due to filtering. (default: None)

Options specific to this tool

(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.