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.