RESEARCH USE
Where CNVkit fits
Derive target and off-target coverage from aligned tumor, normal, or germline BAM files, correct technical biases with a matched normal pool or flat reference, then segment, call, and visualize copy-number estimates. Preserve capture regions, reference build, normal selection, purity and ploidy assumptions, segmentation method, version, and intermediate files, and confirm consequential events with an independent method.
Research tasks
- Estimate copy-number changes from targeted or exome sequencing
- Combine allele frequencies with segmentation and copy-number analysis
- Generate scatter, chromosome, diagram, and tabular outputs
What to evaluate before use
- Platform, capture design, normal reference, tumor purity, and ploidy affect absolute copy-number interpretation. A flat reference is generally less informative than matched normals.
- Segments and calls are statistical estimates, not validated clinical variants. Low coverage, contamination, subclonality, and batch effects can create or obscure events.
Verification note
This entry summarizes the resource's role without assessing scientific accuracy or endorsing its outputs. Features and terms can change; consult the official source before adopting it for consequential work.
copy-number variationsequencing analysis
Last verified: 2026-09-17
Source: official documentation ↗