Copy Number Variation (CNV) Analysis from SNP Array Data

• This code was used to generate CNV calls for the Facebase project
• calls using three tools: VanillaICE, pennCNV, and DNACopy.
• Rather than relying on one algorithm, we seek consensus among the three for more robust results.

Getting Started

Prerequisites

• assumes data have been processed by Illumina GenomeStudio and results stored in FinalReport
• PennCNV
• DNAcopy
• VanillaICE
• ArrayTV
• bedtools

Installing

git clone https://github.com/dpastling/facebase_cnv

Tesing

TODO: find a small example file online TODO: also need support files

Running the code

• modify the config.sh file
• TODO: more info here

License

This project is licensed under the MIT License - see the LICENSE.md file for details

Acknowledgments