Use this skill for genomic circular visualization tasks using the Circos CLI. Applies when the task involves producing Circos plots for genomic data — including karyotype/ideogram rendering, copy number histograms, B-allele frequency (BAF) scatter/line plots, and structural variant or junction link arcs. Do NOT use for chord diagrams of non-genomic data.
Apply this skill when:
Do NOT apply when:
Your Python code prepares files only. The executor runs the Circos CLI after Python succeeds.
Find available files from the input metadata. Common sources:
| Track | Typical file names |
|---|---|
| Karyotype | karyotype*.txt, cleaned_karyotype.* |
| FASTA | *.fasta, *.fa, *.fna, sequence.fasta |
| GFF3 annotations | *.gff3, *.gff |
| Copy number | cleaned_cn., validated_copy_number. |
| BAF | cleaned_baf., validated_baf. |
| Links / junctions | links.txt, cleaned_junctions., validated_junctions. |
See reference/data_formats.md for parsing examples.
If a Circos-format karyotype file already exists (chr - ID Label 0 LENGTH COLOR), copy it. If only a FASTA is available, generate the karyotype from sequence lengths.
Only include tracks for which source data actually exists:
Write results/circos_config/circos.conf. Include only plot/link blocks for tracks that have data. See reference/circos_config_guide.md for a complete template.