varstrat 0.1.0

A tool to annotate VCF files using genome stratification files, targeting difficult regions.

VarStrat

A tool for annotating VCF files using genome stratification files, targeting difficult regions.

Installation

Use the package manager pip to install VarStrat.

pip install varstrat

Usage

To use the tool from the command line:

varstrat input.vcf output.vcf data_source_dir

Final Notes

1. Make Sure the Script is Executable:

   • Ensure stratify.sh is executable by running chmod +x varstrat/stratify.sh.
   • Also, make sure stratify.py is executable by running chmod +x varstrat/stratify.py.

2. Verify the Help Option:

   • Run your script with the -h or --help option to verify it displays the help message correctly:

     varstrat -h