cnvkit-copy-number

Detect somatic copy number variants from WES, WGS, or targeted sequencing BAM files by normalizing coverage and segmenting copy ratios to call amplifications and deletions. The pipeline automates this detection for paired tumor-normal samples.

Estimate tumor purity and ploidy to refine copy number variant calls. The tool integrates purity and ploidy estimation directly into the segmentation and calling process for more accurate somatic mutation detection.

Export copy number variation results in VCF, SEG, and BED formats for downstream analysis and visualization. These standard formats support integration with platforms like cBioPortal and other genomic pipelines.

Integrate copy number variant detection into a custom bioinformatics pipeline using both CLI and Python API interfaces. This allows automated batch processing of paired tumor-normal WES or WGS samples within existing workflows.

Detect somatic copy number variations using paired tumor-normal BAM files. Normal samples are used to normalize coverage and accurately distinguish true somatic amplifications and deletions from sequencing artifacts.

Running cnvkit for copy number variation analysis requires dependencies including matplotlib, pandas, samtools, and R-DNAcopy. These tools support coverage normalization, segmentation, and visualization of sequencing data.