File formats

We’ve tried to use standard file formats where possible in CNVkit. However, in a few cases we have needed to extend the standard BED format to accommodate additional information.

All of the non-standard file formats used by CNVkit are tab-separated plain text and can be loaded in a spreadsheet program, R or other statistical analysis software for manual analysis, if desired.

BED and GATK/Picard Interval List

Note that BED genomic coordinates are 0-indexed, like C or Python code – for example, the first nucleotide of a 1000-basepair sequence has position 0, the last nucleotide has position 999, and the entire region is indicated by the range 0-1000.

Interval list coordinates are 1-indexed, like R or Matlab code. In the same example, the first nucleotide of a 1000-basepair sequence has position 1, the last nucleotide has position 1000, and the entire region is indicated by the range 1-1000.


See the VCF specifications.

CNVkit currently uses VCF files in two ways:

  • To export CNVs, describing/encoding each CNV segment as a structural variant (SV).
  • To plot single-nucleotide variant (SNV) allele frequencies in the scatter and loh commands, or export these allele frequencies to the “nexus-ogt” format.

Target and antitarget bin-level coverages (.cnn)

Coverage of binned regions is saved in a tabular format similar to BED but with additional columns. Each row in the file indicates an on-target or off-target (antitarget, background) bin. Genomic coordinates are 0-indexed, like BED.

Column names are shown as the first line of the file:

  • Chromosome or reference sequence name (chromosome)
  • Start position (start)
  • End position (end)
  • Gene name (gene)
  • Log2 mean coverage depth (log2)

Essentially the same tabular file format is used for coverages (.cnn), ratios (.cnr) and segments (.cns) emitted by CNVkit.

Copy number reference profile (.cnn)

In addition to the columns present in the “target” and “antitarget” .cnn files, the reference .cnn file has the columns:

  • GC content of the sequence region (gc)
  • RepeatMasker-masked proportion of the sequence region (rmask)
  • Statistical spread or dispersion (spread)

The log2 coverage depth is the weighted average of coverage depths, excluding extreme outliers, observed at the corresponding bin in each the sample .cnn files used to construct the reference. The spread is a similarly weighted estimate of the standard deviation of normalized coverages in the bin.

To manually review potentially problematic genes in the built reference, you can sort the file by the “spread” column; bins with higher values are the noisy ones.

It is important to keep the copy number reference file consistent for the duration of a project, reusing the same reference for bias correction of all tumor samples in a cohort. If your library preparation protocol changes, it’s usually best to build a new reference file and use the new file to analyze the samples prepared under the new protocol.

Bin-level log2 ratios (.cnr)

In addition to the BED-like chromosome, start, end and gene columns present in .cnn files, the .cnr file has the columns:

  • Log2 ratio (log2)
  • Proportional weight to be used for segmentation (weight)

The weight value is derived from several sources:

  • The size of the bin relative to the average bin size (for targets or antitargets, separately)
  • For a paired or pooled reference, the deviation of the reference log2 value from neutral coverage (i.e. distance from 0.0)
  • For a pooled reference, the inverse of the variance (i.e. square of spread in the reference) of normalized log2 coverage values seen among all normal samples at that bin.

This calculated value is used to weight the bin log2 ratio values during segmentation. Also, when a genomic region is plotted with CNVkit’s “scatter” command, the size of the plotted datapoints is proportional to each bin’s weight – a relatively small point indicates a less reliable bin.

Segmented log2 ratios (.cns)

In addition to the chromosome, start, end, gene and log2 columns present in .cnr files, the .cns file format has the additional column probes, indicating the number of bins covered by the segment.

The gene column concatenates the gene names of all the bins that the segment covers. The weight column sums the bin-level weights.