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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 doubling, running tumor-only allele-specific calling, or choosing among ASCAT, Sequenza, FACETS, and PureCN.

skills/bioskills/bio-copy-number-allele-specific-copy-number/SKILL.md

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## 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-genome doubling — CNVkit and GATK somatic CNV cannot answer those.