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subclonal-copy-number

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Resolve subclonal copy number, whole-genome doubling, and copy-number tumor evolution from bulk sequencing with Battenberg, TITAN, and MEDICC2. Covers clonal versus subclonal copy-number states, haplotype phasing for subclonal resolution, cancer cell fraction, whole-genome-doubling detection and timing relative to mutations, mirrored subclonal allelic imbalance, and copy-number phylogenies. Use when a tumor is heterogeneous and bulk data shows non-integer copy number, when calling subclonal CNAs, detecting or timing whole-genome doubling, reconstructing copy-number evolution, or deciding between Battenberg and TITAN.

When to use

• resolving subclonal copy number
• detecting whole-genome doubling
• timing whole-genome doubling relative to mutations
• reconstructing copy-number phylogenies
• calling subclonal CNAs
• deciding between Battenberg and TITAN
• resolving mirrored subclonal allelic imbalance
• estimating cancer cell fraction

When not to use

• clonal-only copy number analysis
• single sample phylogeny construction
• analysis without allele-specific data

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