CNVkit attempts to handle chromosomal sex (interchangeably called “gender” in this documentation) correctly throughout the analysis pipelines.

Several commands automatically infer a given sample’s chromosomal sex from the relative copy number of the autosomes and chromosomes X and Y; the status log messages will indicate when this is happening. In most cases the inference can be skipped or overridden by using the -g/--gender option.

The gender command runs and report’s CNVkit’s inference for one or more given samples, and can be used on .cnn, .cnr or .cns files at any stage of processing.

Reference gender

See reference

If you want copy number calls to be relative to a male reference with a single X chromosome but dipoid autosomes, use the -y option everywhere. Otherwise, X and all autosomes will be considered normally diploid. Chromosome Y will be considered haploid in either case.

Gender in calling absolute copy number

See call

Plots and gender

diagram adjusts the sex chromosomes for sample and reference gender so that gains and losses on chromosomes X and Y are highlighted and labeled appropriately.

scatter and heatmap do not adjust the sex chromosomes for sample or reference gender.


Why does chromosome X/Y show a gain/loss?

The copy number status of sex chromosomes may be surprising if you are unsure about the gender of the samples and reference used:

  • Female samples normalized to a male reference will show a doubling of chromosome X (log2 value about +1.0) and complete loss of chromosome Y (log2 value below -3.0, usually far below).
  • Male samples normalized to a female reference will show a single-copy loss of chromosome X (log2 value about -1.0). The chromosome Y value should be near 0.0, but the log2 values may be noisier and less reliable than on autosomes.

In the output of the diagram, call, and export commands, the X or Y copy number may be wrong if the gender of the reference (-y/--male-reference) or sample (-g) was not specified correctly. If sample gender was not specified on the command line, check the command’s logged status messages to see if the sample’s gender was guessed incorrectly.

After you’ve verified the above, the CNV might be real.

CNVkit is not detecting my sample’s gender correctly. What can I do?

In lower-quality samples, particularly tumor samples analyzed without a robust reference (see Tumor analysis), there may be many bins with no coverage which bias the segment means. Try repeating the segment command with the --drop-low-coverage option if you did not do so originally.

See also: