diff --git a/README.md b/README.md new file mode 100644 index 0000000000000000000000000000000000000000..7221a51805b3b3195eddf1b6cb196f5aa49ba1e5 --- /dev/null +++ b/README.md @@ -0,0 +1,27 @@ +# Popsimul + +## Description + +## Requirements +python 3 + +## Running popsimul + +``` python noisyplotype -o test1511.vcf -n 10 -s 44000000 -cM 180 -d 0.0058 -a 3 -m 10 -eA 0.03 -eB 0.05``` + +### Parameters description + +You can see all parameters by running this command +``` python noisyplotype -h``` + +| Short | Long | Description | Default value | +|---|---|---|---| +| -o | --output | Name for the 3 generated files : [output].vcf, [output]_errors.vcf, [output]_Breakpoints.csv | popsimul | +| -n | --nb_individuals | number of individuals | 10 | +| -s | --chr_size | chromosome size | 4000000| +| -cM | --cM_size | size of genetic map | 180 | +| -d | --marker_density | marker density| 0.005 | +| -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 |