README.md

Dependencies:

• R/3.6.1

Execution: Rscript CNV_profiler.R --argument value

Required arguments: --path = "Path to .cov files from Bismark" --tumor = "Prefix of Tumor .cov files" --normal = "Prefix of Normal .cov files" --chrom_sizes = "File with Chromosome Sizes" --resolution = "One of 'chromosome' or 'sliding'. [DEFAULT:chromosome]" --window_size = "If resolution = 'sliding', size of window (in MB) [DEFAULT=100]" --sliding_by = "If resolution = 'sliding', sliding by (in MB) [DEFAULT=100]" --output = "Prefix of Results" --region = "Return results of a specified region , Format: 'chr1:1200:1400' "