CNV analysis on Illumina NGS data with PLINK or other toolsets

Question

[plague]

I am looking to wrok with CNV calls made from WGS data by Illumina's 'new' Canvas & Manta tools. Has anyone used PLINK for downstream analysis of the calls made by these tools? Or any other toolset that they have success with? Would be great to hear people's views or receive any links in this area.