CNVision

CNVision is a Perl script that runs Illumina genotyping data (all chips from 300k to latest Omni) through PennCNV, QuantiSNPv2.3 and GNOSIS (an in-built algorithm). It merges the results and assesses the quality of the raw data. CNVision can also identify de novo CNVs in family-based data using a highly accurate algorithm that considers the possibility of CNVs in either parent based on the raw genotyping data.

The script is optimized to work in a UNIX-based environment; it should work in Windows, however running the PennCNV component gives errors with the newer versions of PennCNV.

CNVision was written to analyze data for the Simons Simplex Collection (SSC) autism data. A fill description of methods are given in the following paper which can be used to reference CNVision:
http://www.ncbi.nlm.nih.gov/pubmed/21658581