Copy-Number-Variations Simulation: Simulation for high-throughput sequencing (HTS) data
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Type Name Latest commit message Commit time
Failed to load latest commit information.


This is a simulation that can generate high-throughput sequencing (HTS) data (BAM file format) for copy number variations such as deletion, inversion, tandem duplication, inverted duplication, interspersed direct duplication.



python -h

usage: [-h] [--out OUT] [--chr CHR] ref n c

positional arguments:
  ref         reference genome (fasta file), e.g. hg38.fa
  n           number of variations, e.g. 1200
  c           sequencing coverage, e.g. 10

optional arguments:
  -h, --help  show this help message and exit
  --out OUT   output directory, default is the current directory
  --chr CHR   name of the chromosome that will contain the CNVs, default =


python --chr 1 --out out human_g1k_v37_gatk.fasta 1200 10