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copy-ratio-segmentation

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Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.

When to use

• choosing a segmentation algorithm
• correcting depth bias
• diagnosing oversegmentation
• diagnosing mis-centered baseline
• tuning CBS parameters
• tuning HMM parameters
• understanding fragmented segments
• understanding shifted segments

When not to use

• allele-specific copy number analysis requiring BAF

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