Description

Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data.

Input

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

bam (file)

BAM/CRAM/SAM file

*.{bam,cram,sam}

meta2 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

fasta (file)

Assembly FASTA file

*.{fasta}

meta3 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

gtf (file)

Annotation GTF file

*.{gtf}

meta4 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

blacklist (file)

Blacklist file

*.{tsv}

meta5 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

known_fusions (file)

Known fusions file

*.{tsv}

meta6 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

structural_variants (file)

Structural variants file

*.{tsv}

meta7 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

tags (file)

Tags file

*.{tsv}

meta8 (map)

Groovy Map containing reference information e.g. [ id:'test' ]

protein_domains (file)

Protein domains file

*.{gff3}

Output

Name
Description
Pattern

meta (map)

Groovy Map containing sample information e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

fusions (file)

File contains fusions which pass all of Arriba's filters.

*.{fusions.tsv}

fusions_fail (file)

File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue.

*.{fusions.discarded.tsv}

Tools

arriba Documentation

Fast and accurate gene fusion detection from RNA-Seq data

https://github.com/suhrig/arribadoi: 10.1101/gr.257246.119License: MIT
Authors