A Python-based whole-genome haplotype-resolution copy number variation simulator.
git clone https://github.com/sunjh22/CNV-simulator.git
cd CNV-simulator
Download ART_illumina and put it into environment path.
wget -O art.tgz https://www.niehs.nih.gov/research/resources/assets/docs/artbingreatsmokymountains04.17.16linux64.tgz
tar -xvzf art.tgz -C ART/
echo "export PATH=PATH:~/ART/art_bin_GreatSmokyMountains" >> .bashrc
source .bashrc
Note: Following reference genome must be from UCSC.
CNV-simulator has three modes:
-
No input CNV list is provided, CNV-simulator will generate one and simulate CNVs based on it.
./cnv_simulator.py -o /path/to/store/simulated/data -a prefix_of_sample -c desired_coverage reference_genome resource/access-excludes.hg38.analysisSet.bed -
An input CNV list is provided in the bed format with four columns: chrom start end cn, CNV-simulator directly simulate CNVs based on it.
./cnv_simulator.py -o /path/to/store/simulated/data -a prefix_of_sample -i /path/to/a/cnv/list/file -c desired_coverage reference_genome resource/access-excludes.hg38.analysisSet.bed -
An input CNV list is provided as in mode 2, but users want to simulate new CNVs on top of the existed ones.
./cnv_simulator.py -o /path/to/store/simulated/data -a prefix_of_sample -i /path/to/a/cnv/list/file -A True -c desired_coverage reference_genome resource/access-excludes.hg38.analysisSet.bed
Users could specify the number of CNVs to be simulated (-n), minimum (-b), maximum (-B) and lambda (-e) of CNV length, lambda is the parameter of exponential distribution that CNV length follows.
Usage: cnv_simulator [-h] [-v] [-o OUTPUT_DIR] [-a PREFIX] [-l READ_LENGTH]
[-i CNV_LIST] [-A APPEND_LIST] [-c COVERAGE]
[-n CNV_NUMBER] [-b CNV_MINIMUM_LENGTH]
[-B CNV_MAXIMUM_LENGTH] [-e CNV_EXPO_SCALE]
[-p AMPLIFY_PROP]
genome access
Simulate whole-genome level haplotype-resolved CNVs and generate NGS reads
Positional arguments:
genome reference genome file in fasta format
access genomic accessible region file
Optional arguments:
-h, --help show this help message and exit
-v, --version Show program's version number and exit.
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
a name to be used to create the output directory
(overrides existing directory with the same name).
(default: tmp_simulaiton)
-a PREFIX, --prefix PREFIX
prefix of simulated genome and fastq files (default:
sample)
-l READ_LENGTH, --read_length READ_LENGTH
read length (bp) (default: 150)
-i CNV_LIST, --cnv_list CNV_LIST
path to a CNV list file in BED format chr | start |
end | cn. If not passed, it is randomly generated
using CNV list parameters below (default: None)
-A APPEND_LIST, --append_list APPEND_LIST
generate some new CNVs and append them into the user-
provided CNV list (default: False)
-c COVERAGE, --coverage COVERAGE
coverage for reads simulation (default: 1)
CNV list parameters:
parameters to be used to generate CNV list if CNV list is not passed
-n CNV_NUMBER, --cnv_number CNV_NUMBER
the number of CNVs to be simulated (default: 200)
-b CNV_MINIMUM_LENGTH, --cnv_minimum_length CNV_MINIMUM_LENGTH
minimum length of each CNV region (default: 5000)
-B CNV_MAXIMUM_LENGTH, --cnv_maximum_length CNV_MAXIMUM_LENGTH
maximum length of each CNV region (default: 2000000)
-e CNV_EXPO_SCALE, --cnv_expo_scale CNV_EXPO_SCALE
scale of a exponential distribution for simulating the
length of CNV (default: 200000)
-p AMPLIFY_PROP, --amplify_prop AMPLIFY_PROP
percentage of amplifications in range [0.0: 1.0].
(default: 0.5)
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