/arriba

Fusion caller which runs off of STAR bam

Primary LanguageWDL

arriba

Workflow that takes the Bam output from STAR and detects RNA-seq fusion events. It is required to run STAR with the option --chimOutType 'WithinBAM HardClip Junctions' as per https://github.com/oicr-gsi/star to create a BAM file compatible with both the arriba and STARFusion workflows. For additional parameter suggestions please see the arriba github link below.

Dependencies

Usage

Cromwell

java -jar cromwell.jar run arriba.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
inputBam File STAR BAM aligned to genome
indexBam File Index for STAR Bam file
outputFileNamePrefix String Prefix for filename
reference String Reference id, i.e. hg38 (Currently the only one supported)

Optional workflow parameters:

Parameter Value Default Description
structuralVariants File? None path to structural variants for sample

Optional task parameters:

Parameter Value Default Description
runArriba.draw String "$ARRIBA_ROOT/bin/draw_fusions.R" path to arriba draw command
runArriba.threads Int 8 Requested CPU threads
runArriba.jobMemory Int 64 Memory allocated for this job
runArriba.timeout Int 72 Hours before task timeout

Outputs

Output Type Description Labels
fusionsPredictions File {'description': 'Fusion output tsv', 'vidarr_label': 'fusionPredictions'}
fusionDiscarded File {'description': 'Discarded fusion output tsv', 'vidarr_label': 'fusionDiscarded'}
fusionFigure File {'description': 'PDF rendering of candidate fusions', 'vidarr_label': 'fusionFigure'}

Commands

This section lists command(s) run by arriba workflow

  • Running arriba

Run the program on bam output from STAR and detects RNA-seq fusion events


      arriba 
      -x INPUT_BAMS 
      -o OUTPUT_PREFIX.fusions.tsv -O OUTPUT_PREFIX.fusions.discarded.tsv 
      -d STRUCTURAL_VARIANTS (Optional) -k COSMIC (Optional) -t KNOWN_FUSIONS 
      -a GENOME -g GENCODE_REFERENCE_FILE -b BLACK_LIST -p DOMAINS

      Rscript DRAW --annotation=GENCODE_REFERENCE_FILE --fusions=OUTPUT_PREFIX.fusions.tsv 
      --output=OUTPUT_PREFIX.fusions.pdf --alignments=INPUT_BAM 
      --cytobands=CYTOBANDS --proteinDomains=DOMAINS

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)