A tool to annotate VCF files using genome stratification files, targeting difficult regions.
A tool for annotating VCF files using genome stratification files, targeting difficult regions.
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.
Use the package manager pip to install VarStrat.
pip install varstrat
To use the tool from the command line:
varstrat --input_vcf input.vcf --output_vcf output.vcf --data_source data_source
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.
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.
FAQs
A tool to annotate VCF files using genome stratification files, targeting difficult regions.
We found that varstrat demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 1 open source maintainer collaborating on the project.
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