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.

Marko Marinkovic