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bio-copy-number-allele-specific-copy-number

Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome

BioTender-maxgithub.com/BioTender-maxGitHub ↗
claude-codeNOASSERTION
Install
npx skills add BioTender-max/awesome-bio-agent-skills --skill allele-specific-copy-number --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

Facts
Files in the skill folder: 3
SKILL.md size: 16 KB
Bundled scripts: none
Path: skills/bioskills/allele-specific-copy-number/SKILL.md
Open the folder on GitHub →
Where it comes from
Stars: 135
Language: Python

Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.

From the SKILL.md

## Version Compatibility Reference examples tested with: ASCAT 3.1+, Sequenza 3.0+ (sequenza-utils 3.0+), FACETS 0.6+ (snp-pileup), PureCN 2.6+, R 4.3+, Python 3.10+. Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('ASCAT')` / `'sequenza'` / `'facets'` / `'PureCN'`, then `?function` - CLI: `sequenza-utils --version`, `snp-pileup --help` Sequenza 3.0 depends on the `copynumber` Bioconductor package, REMOVED from Bioconductor 3.18+ (2023). Install a maintained fork (`ShixiangWang/copynumber` or `igordot/copynumber`) before Sequenza will load. ASCAT's GC-correction function was renamed across 2.x->3.x (`ascat.GCcorrect` -> `ascat.correctLogR`) — verify against the installed version. # Allele-Specific Copy Number **"How many copies of each allele, in what fraction of cells, at what tumor purity"** -> Jointly model read depth and B-allele frequency to fit tumor purity, ploidy, and integer major/minor copy number per segment. Depth alone gives only *relative* copy ratio; depth + BAF gives *absolute* allele-specific copy number. This skill is required whenever the question involves LOH, absolute copy number, purity, ploidy, or whole-ge

What's inside
Steps it walks through
  1. Version Compatibility
  2. The Identifiability Problem — Why This Is Hard
  3. Caller Taxonomy
  4. Decision Tree by Data Type
  5. FACETS — Tumor-Normal Allele-Specific CN
  6. Sequenza — Exome Tumor-Normal
  7. ASCAT — WGS / SNP Array
  8. PureCN — Tumor-Only
  9. Failure Modes
  10. ASCAT defaults to ~100% purity on a near-diploid genome
  11. FACETS hyperfragmentation from too-low cval
  12. Integer-multiple ploidy flip
  13. Sequenza fails to load / picks a near-diploid optimum
  14. Low-purity death zone
Ships with 2 files
  • examples/run_facets.R
  • usage-guide.md
Commands it runs
Step 1: pileup at dbSNP common sites (normal first, then tumor)
snp-pileup -g -q15 -Q20 -P100 -r25,0 dbsnp_common.vcf.gz \
sample.snp_pileup.csv.gz normal.bam tumor.bam
sequenza-utils bam2seqz -n normal.bam -t tumor.bam --fasta ref.fa \
sequenza-utils seqz_binning --seqz sample.seqz.gz -w 50 -o sample.bin.seqz.gz
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About this skill
What does the bio-copy-number-allele-specific-copy-number skill do?

Infer integer allele-specific copy number, tumor purity, and ploidy from tumor sequencing by jointly modeling read depth (logR) and B-allele frequency (BAF) with ASCAT, Sequenza, FACETS, PURPLE, and PureCN (tumor-only). Covers the purity-ploidy identifiability problem, the diploid-baseline (dipLogR) anchor, major/minor copy number, loss of heterozygosity, sunrise/contour fit diagnostics, and reconciliation of conflicting fits. Use when tumor analysis needs absolute copy number rather than relative log2, when estimating purity and ploidy, calling LOH or copy-neutral LOH, resolving whole-genome

How do I install it?

Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill allele-specific-copy-number --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.

Where does this skill come from?

From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.

Is a popular skill a good skill?

Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.

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