Workflow

Click the nodes to obtain details about each step.

Circle calls

Statistics

If the workflow has been executed in cluster/cloud, runtimes include the waiting time in the queue.

Configuration

Configuration files
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calling:
  samples: config/samples.tsv
  units: config/units.tsv

  reference:
#     name: "grch38_with_plasmid_replacements"
#     path: "resources/grch38_with_plasmid_replacements.fasta"
    name: "grch38_with_alk_myc_plasmids"
    path: "resources/grch38_with_alk_myc_plasmids.fasta"

  min_read_depth: 2
  min_split_reads: 5
  max_paths_per_component: 15
  max_deletion_length: 10000

  # TODO: actually use these settings
  filter:
    fdr-control:
      threshold: 0.05
      local: true
      events:
        circular:
          varlociraptor:
            - present

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