What are the best tools/practices for CNV detection/analysis?

[Irina Astrovskaya]

I am looking for the current state-of-the-art tools/practices for CNV (structural variation) detection/analysis for family (trio) data produced by Illumina.

I will have data obtained on Illumina SNP arrays as well as from Illumina whole exome sequencing and whole-genome sequencing.
What would be the best tools to apply for each technology?

Any advice/suggestion is highly appreciated

Thank you!