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cnv-visualization

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Visualize copy number profiles, segments, allele-specific tracks, and cohort patterns from CNVkit, GATK, ASCAT, FACETS, Sequenza, and other callers. Covers genome-wide and per-chromosome log2 scatter plots, B-allele-frequency/minor-allele-fraction tracks, ideograms, cohort heatmaps, circos views, and caller-native plots. Use when creating publication CNV figures, choosing which plot answers a given question, diagnosing a wrong diploid baseline visually, displaying loss of heterozygosity, or deciding what depth-only plots cannot reveal.

When to use

• creating publication CNV figures
• choosing which plot answers a given question
• diagnosing a wrong diploid baseline visually
• displaying loss of heterozygosity
• deciding what depth-only plots cannot reveal
• genome-wide and per-chromosome log2 scatter plots
• B-allele-frequency/minor-allele-fraction tracks
• ideograms, cohort heatmaps, circos views, and caller-native plots

When not to use

• showing loss of heterozygosity with depth-only log2 plots
• showing tumor purity with depth-only log2 plots

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