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Copy Number Variations (CNV) Simulator
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CNV Simulator

In genomics, Copy Number Variations (CNVs) is a type of structural variation in a genome where sections of the genome are repeated. The number if repetitions (duplications) varies between individuals in the human population.

The Copy Number Variation Simulator (CNV Sim) is a tool used to generate a set of artificial DNA fragments for Next Generation Sequencing (NGS) read simulation. When aligned back to the reference genome, the artificial generated reads show variations in the CNV regions. Variations can be either amplifications of deletions.

CNV-Sim offers two types of simulation:

  1. CNV simulation in whole genome. CNV-Sim wraps the functionality of ART to introduce variations in the genome.
  2. CNV simulation in whole exome. CNV-Sim wraps the functionality of Wessim to introduce variations in the targets.

How to run:

docker run -v <absolute_local_path_to_input_directory>:/input nabavilab/cnv-sim ./ -o /input/<simulation_name> [OPTIONS] {genome, exome} /input/<genome_file> [/input/<target_file>]


  • <absolute_local_path_to_input_directory> is the directory where the required input files exist (genome.fa and target.bed if using exome simulation); MUST be absolute path
  • <simulation_name> is used as the name of the output folder in your data directory, where the output of CNV Sim will be saved
  • <genome_file> is the FASTA file name for the genome reference
  • <target_file> is the BED file name for the targets (only if using exome as the simulation type)


    Refer to GitHub documentation for more details about the options.
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