Cnvkit
- cnvkit-access(1) List the locations of accessible sequence regions in a FASTA file.
- cnvkit-antitarget(1) Derive off-target ("antitarget") bins from target regions.
- cnvkit-autobin(1) Quickly calculate reasonable bin sizes from BAM read counts.
- cnvkit-batch(1) Run the complete CNVkit pipeline on one or more BAM files.
- cnvkit-bintest(1) Test for single-bin copy number alterations.
- cnvkit-breaks(1) List the targeted genes in which a copy number breakpoint occurs.
- cnvkit-call(1) Call copy number variants from segmented log2 ratios.
- cnvkit-coverage(1) Calculate coverage in the given regions from BAM read depths.
- cnvkit-diagram(1) Draw copy number (log2 coverages, segments) on chromosomes as a diagram.
- cnvkit-export(1) Convert CNVkit output files to another format.
- cnvkit-fix(1) Combine target and antitarget coverages and correct for biases.
- cnvkit-genemetrics(1) Identify targeted genes with copy number gain or loss.
- cnvkit-heatmap(1) Plot copy number for multiple samples as a heatmap.
- cnvkit-import-picard(1) Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn files.
- cnvkit-import-rna(1) Convert a cohort of per-gene log2 ratios to CNVkit .cnr format.
- cnvkit-import-seg(1) Convert a SEG file to CNVkit .cns files.
- cnvkit-import-theta(1) Convert THetA output to a BED-like, CNVkit-like tabular format.
- cnvkit-metrics(1) Compute coverage deviations and other metrics for self-evaluation.
- cnvkit-reference(1) Compile a coverage reference from the given files (normal samples).
- cnvkit-reference2targets(1) Extract target and antitarget BED files from a CNVkit reference file.
- cnvkit-scatter(1) Plot probe log2 coverages and segmentation calls together.
- cnvkit-segment(1) Infer copy number segments from the given coverage table.
- cnvkit-segmetrics(1) Compute segment-level metrics from bin-level log2 ratios.
- cnvkit-sex(1) Guess samples' sex from the relative coverage of chromosomes X and Y.
- cnvkit-target(1) Transform bait intervals into targets more suitable for CNVkit.
- cnvkit(1) a command-line toolkit for copy number analysis.