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allele-specific-copy-number

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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.

When to use

• absolute copy number
• estimating purity and ploidy
• calling LOH or copy-neutral LOH
• resolving whole-genome doubling
• tumor-only allele-specific calling
• choosing among ASCAT, Sequenza, FACETS, and PureCN
• subclonal CN
• clonal evolution

When not to use

• relative log2 copy number
• relative gain/loss
• CNVkit analysis
• GATK somatic CNV

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