snpsnip 0.0.3

An interactive VCF filtering tool

SNPSnip - An interactive VCF Filtering Tool

SNPSnip is a command-line tool with an interactive web interface for filtering VCF files in multiple stages.

Prerequisites

• Python 3.8 or higher
• bcftools must be installed and available in your PATH

Install from source

pip install git+https://github.com/gekkonid/snpsnip.git

Usage

Basic usage:

snpsnip --output-dir filtered_results --vcf input.vcf.gz --maf 0.05 --max-missing 0.1 --min-qual 30

If you need, you can change the web server settings:

snpsnip --vcf input.vcf.gz --host 0.0.0.0 --port 8080

Workflow

1. Initial Processing: SNPSnip extracts a random subset of SNPs passing basic filters.
2. Sample Filtering: The web UI allows you to filter samples based on quality metrics and PCA clustering.
3. Variant Filtering: For each sample group, set filtering thresholds for various metrics.
4. Final Processing: The tool applies your filters to the full VCF file to generate filtered outputs.

License

MPL2