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Release note

Recently published apps

We have published the CNVkit 0.9.9 toolkit for inferring and visualizing copy number from high-throughput DNA sequencing data. The toolkit includes the following tools:

  • CNVkit breaks lists the targeted genes in which a segmentation breakpoint occurs.
  • CNVkit access calculates the sequence-accessible coordinates in chromosomes from the given reference genome.
  • CNVkit diagram draws copy number or segments on chromosomes as an ideogram.
  • CNVkit export bed converts segments to a BED file.
  • CNVkit export vcf converts segments to a VCF file.
  • CNVkit segmetrics calculates summary statistics of individual segments.
  • CNVkit scatter plots bin-level log2 coverages and segmentation calls together.
  • CNVkit metrics calculates the spread of bin-level copy ratios from the corresponding final segments.
  • CNVkit heatmap draws copy number for multiple samples as a heatmap.
  • CNVkit genemetrics identifies targeted genes with copy number gain or loss above or below a threshold.
  • CNVkit call calls absolute integer copy number for each segment in segmented log2 ratio estimates.
  • CNVkit batch is a copy number calling pipeline wrapped into a single tool.