datasets.yaml

# define which datasets will be evaluated in the benchmark 

# This is an example of dataset definition:
dataset1:
  include: true   # true to include this dataset in the analysis, false otherwise
  bams_dir: "/yourPath/bams/"   # folder where bams files (.bai indexes) are stored
  bed_file: "/yourPath/bed5.bed"   # bed file defining ROIs. It must be sortered by chr and start position, and 4th column must contain only gene symbol. (See examples folder)
  fasta_file: "/yourPath/GRCh37_Ensembl_67.fa"   # genome fasta file
  validated_results_file: "/yourPath/MLPAresults.txt"    # file containing results obtained using a orthogonal method (MLPA or aCGH) (See examples folder)
  validated_results_file_format: "icr"   # format of validated results file: icr or panelcn
  read_length: 101   # read length used when sequencing