CNVkit attempts to handle chromosomal sex 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
The sex 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.
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.
Plots and sex chromosomes¶
diagram adjusts the sex chromosomes for sample and reference sex so that gains and losses on chromosomes X and Y are highlighted and labeled appropriately.
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 sex 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 sex of the reference
--male-reference) or sample (
-x) was not specified correctly. If
sample sex was not specified on the command line, check the command’s logged
status messages to see if the sample’s sex was guessed incorrectly.
After you’ve verified the above, the CNV might be real.
CNVkit is not detecting my sample’s sex 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: https://www.biostars.org/p/210080/