pipelines implemented for various read-depth CNV calling tasks, including:

• RD_setup: performing QC, GC-normalization, parameter fitting, browser track generation and DenseTrackSet windowed copy number estimation
• GC_analysis: asssessing GC_associated coverage biases
• dCGH: calling CNVs using dCGH

Quick setup:

git clone https://github.com/eichlerlab/RD_pipelines.git --recursive
cd RD_pipelines
. env.conf
make