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PopSimul

Authors

Cécile Triay (IRD)
Alice Boizet (CIRAD)
Mathias Lorieux (IRD)
Mathieu Triay (Atelier Triay)

Description

This tool enables to simulate a VCF of a bi-parental population. It can be used to produce a VCF under controlled conditions with setting parameters such as average depth, marker density and expected error rate. It produces 3 VCF files:

  • simulated genotypes with no noise and no sequencing error
  • simulated genotypes with noise but no sequencing error
  • simulated genotypes with noise and sequencing error

The Breakpoints csv file contains the positions of exact genotypes transitions based on the simulated genotype with no noise and no sequencing error.

This tool has been used to test NOISYmputer (https://gitlab.cirad.fr/noisymputer/noisymputerstandalone) to compare exact Breakpoints position to Breakpoints positions determined on imputed data.

Requirements

python 3

Running popsimul

python popsimul.py -o test1511.vcf -ni 10 -s 44000000 -cM 180 -nm 220000 -a 3 -m 10 -eA 0.03 -eB 0.05

Parameters description

You can see all parameters by running this command
python popsimul.py -h

Short Long Description Default value
-o --output Name for the generated files : [output].vcf, [output]_errors.vcf, [output]_noise_errors.vcf, [output]_Breakpoints.csv popsimul
-ni --nb_individuals number of individuals 10
-bp --chr_bp chromosome size 44000000
-cM --cM_size size of genetic map 180
-nm --nb_markers number of markers 220000
-a --average_depth average depth 3
-m --max_depth max depth 10
-eA --error_rate_A error rate for A 0.05
-eB --error_rate_B error rate for B 0.05