CNV and SV analysis of Complete Genomics data

[augustblackburn]

Any suggestions for tools/pipelines to identify CNVs and SVs from Complete Genomics data? Anyone with any experience doing this?

Has anyone tested how well any of the following tools work when using the sam/bam files created by the evidence2sam function in CGAtools?

CNVnator
RDXplorer
BreakDancer
GASV

Fell free to comment on anything you have tried.
I will update this thread as I try different tools.

[arcolombo698]

The only thing I have learned is that CNV-seq is only useful if you used Solid alignment tools, or BLAT alignment tools, and CNV-seq is not useful for mouse data, but only human and chicken.