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 --recursive
cd RD_pipelines
. env.conf
make