README.md

# PopSimul

## Description

## 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 3 generated files :  [output].vcf, [output]_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 |