varstrat

VarStrat

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

Description

VarStrat is designed to annotate VCF (Variant Call Format) files using genome stratification files. It focuses on difficult regions, providing comprehensive annotations to aid in variant analysis.

Installation

Use the package manager pip to install VarStrat.

pip install varstrat

Usage

To use the tool from the command line:

varstrat --input_vcf input.vcf --output_vcf output.vcf --data_source data_source

Command-line Options

usage: varstrat [-h] --input_vcf INPUT_VCF --output_vcf OUTPUT_VCF --data_source DATA_SOURCE

A tool for stratifying genetic variants.

optional arguments:
  -h, --help            show this help message and exit
  --input_vcf INPUT_VCF
                        Path to the input VCF file. The file can be in VCF or VCF.GZ format.
  --output_vcf OUTPUT_VCF
                        Path to the output VCF file. The output will be a .vcf file.
  --data_source DATA_SOURCE
                        Path to the data source directory containing stratification regions.

Parameters Explanation

• input_vcf: Path to the input VCF file. The file can be in .vcf or .vcf.gz format.

• output_vcf: Path to the output VCF file. The output will be a .vcf file.

• data_source: Path to the data source directory containing stratification regions. The directory should have the following structure:

  data_source/
  ├── Region_name_1
  │   ├── sub_region_1.bed.gz
  │   ├── sub_region_2.bed.gz
  ├── Region_name_2
  │   ├── sub_region_1.bed.gz
  │   ├── sub_region_2.bed.gz
  ...
  

  Each region is represented by a folder containing one or more .bed.gz files that specify sub-regions.

  You can check at genome-stratification for more information about the data source.