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Panel commands

Target panels define which genes/regions drive target, CNV, and fusion analyses and which packaged BED files ROBIN uses. Built-in panels ship with the install; you can add custom panels from BED files.

Commands:

All require the interactive disclaimer (I agree).

robin list-panels

Lists built-in panels (rCNS2, AML, PanCan, …) and custom panels registered in robin.resources.

robin list-panels

Use the printed names with robin workflow --target-panel and robin utils sequencing-files --panel.

robin add-panel

Register a new panel from a BED file.

robin add-panel /path/to/panel.bed MyPanelName

BED format

  • At least 4 columns: chrom, start, end, gene (or comma-separated genes).
  • 6-column BED is allowed (score, strand).
  • Regions spanning multiple genes can list comma-separated gene symbols in the name column.

Options

Flag Meaning
--validate-only Check the BED only; do not copy files into resources.

Reserved names

You cannot use rCNS2, AML, or PanCan as custom names.

What ROBIN stores

  • Processed unique-gene BED: {PanelName}_panel_name_uniq.bed under robin.resources.
  • Original upload copy: {PanelName}_panel_source.bed (for traceability and sequencing-files).

If a panel with the same name already exists, the command fails until you remove-panel.

robin remove-panel

Remove a custom panel (not built-ins).

robin remove-panel MyPanelName
robin remove-panel MyPanelName --force
Flag Meaning
-f / --force Skip the yes confirmation (destructive).

Built-in panels cannot be removed.

Using panels in a workflow

robin workflow /data/bams \
  -w target,cnv,fusion \
  --target-panel MyPanelName \
  --center Sherwood \
  -d ~/results \
  --reference ~/references/hg38.fa