Correct way to get SV BED/VCF

[Zenerzul]

I am interested in copy number variants in whole exome sequencing data and I need to get bed-file and vcf-file to inspect those. As stated in the instruction, I can achieve that by using export bed/vcf command on cns-file.

What would be the difference between using cnvkit.py export on .cns and .call.cns files after default cnvkit.py batch pipeline to get list of SV/CNV?

[etal]

With .cns, you'd get all regions, and with .call.cns, depending on the options, you could filter out the copy-neutral regions in the output file.

[Zenerzul]

Thx for the quick response!