Running cnvkit batch with -y parameter

Question

[alyza]

I have prostate WGS samples and ran the CNVkit pipeline, however, when plotting the diagram it assumes female for some of the samples. I than re-ran the pipeline using the -y parameter and when it plotted the diagram, it assumes all samples are female. Does the -y parameter change the actual calculation for the autosomes or takes into account the sex chromosome ratio in any way?

Answer 1

[Eric T.]

If you use -y anywhere, you have to use it everywhere. Did the diagram plot come from the same batch run where -y was used? If not, you can just run diagram again and add -y.

Full details here: https://cnvkit.readthedocs.io/en/stable/sex.html