ExomeDepth_pipeline

Our approach for calling CNVs on NGS using ExomeDepth (https://CRAN.R-project.org/package=ExomeDepth)

Based on https://github.com/ericminikel/ngs-scripts

Usage examples:

# cnv_detection_ED.R -i /DB/Path/DB.file  (-b bamlist.txt/-s file.bam) -o /output/path/ -v
# create_ExomeDepth_DB.R -b bamlist.txt -o /output/path/ -v
# runExomeDepth.r -b bamlist.txt -o /output/path/ -v