copy-number-cnvkit-analysis - Call copy-number variants with CNVkit
Detect relative somatic and germline copy-number variants from targeted, exome, and whole-genome sequencing using CNVkit read-depth analysis.
Tags
Updated: 2026-10-01Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Normalize read-depth coverage
- Build pooled normal references
- Segment log2-ratio profiles
- Call copy-number states
- Apply purity-aware integer calling
- Reconcile depth-based calls
Inputs
- Tumor BAM files
- Normal BAM files
- Target BED files
- Reference FASTA files
- Gene annotation files
- Access BED files
- Pooled reference CNN files
- Tumor VCF files
- Tumor purity values
- Ploidy values
Outputs
- CNVkit reference CNN files
- Coverage CNN files
- Copy-ratio CNR files
- Segment CNS files
- Copy-number call files
- Scatter plots
- Diagram plots
Requirements
- CNVkit 0.9.10 or later
- samtools 1.19 or later
- bedtools 2.31 or later
- Python 3.10 or later
- R 4.3 or later
- DNAcopy 1.76 or later
- pomegranate for HMM segmentation
- Bioconductor DNAcopy for CBS segmentation