📦 cnvkit

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• cnvkit(1)a command-line toolkit for copy number analysis.✨
• 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. If both the raw probes and segments are given, show them side-by- side on each chromosome (segments on the left side, probes…✨
• cnvkit-export(1)Convert CNVkit output files to another format.✨
• cnvkit-fix(1)Combine target and antitarget coverages and correct for biases. Adjust raw coverage data according to the given reference, correct potential biases and re-center.✨
• 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. The input file is generated by the PER_TARGET_COVERAGE option in the CalculateHsMetrics script in Picard tools. If 'antitarget'…✨
• 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. Equivalently, use the THetA results file to convert CNVkit .cns segments to integer copy number calls.✨
• 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.✨